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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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Bug in Footprint function #593

Closed summer-tao closed 3 years ago

summer-tao commented 3 years ago

Dear Tim,

I have two scATAC-seq samples. I isolate 3 clusters from one sample(total 7 clusters), and then integrate it with another sample. I want to conduct footprint analysis. But I will get an error. I have no idea how to check what's wrong. Could you help me, please? By the way, the Footprint analysis works in another Object.

Best, Tao.

test4 <- Footprint(
+   object = neoThy,
+   motif.name = c("ZBTB14","EGR3","RORA"),
+   genome = BSgenome.Mmusculus.UCSC.mm10,
+   fill=TRUE
+ )
Computing Tn5 insertion bias
Extracting reads in requested region
Extracting reads in requested region
**Error in rbindlist(l, use.names, fill, idcol) : 
  Item 2 has 6 columns, inconsistent with item 1 which has 7 columns. To fill missing columns use fill=TRUE.**
timoast commented 3 years ago

Can you provide the full code you're running and the output of sessionInfo()?

FYI, fill is not a parameter in the Footprint() function. See the function documentation for more information.

summer-tao commented 3 years ago

Thank you Tim. Here is the code.

#Firslty I isolate 3 cluster from a seurat object V4 and then combined with another object V4.
V4 <- TV4[ ,TV4@active.ident %in% c("0","1", "6")]
V4 <- V4 [,V4 $dataset %in% c("neoTV4")]

#combined with another seurat
combined <- merge(
  x = V6,
  y = V4,
  add.cell.ids = c("V6", "V4"),
  project = "SeuratProject"
)
combined <- RunTFIDF(combined) %>% FindTopFeatures(min.cutoff = 20) %>% 
  RunSVD() %>% RunUMAP(dims = 2:30, reduction = 'lsi')

# compute gene activities
gene.activities <- GeneActivity(combined ,assay = "ATAC",
                                extend.upstream = 2000,
                                extend.downstream = 200,
                                verbose = TRUE)
rownames(gene.activities)[duplicated(rownames(gene.activities))]
#There is a duplicated gene
rownames(gene.activities)
#remove the duplicated
gene.activities <- gene.activities[rownames(gene.activities)!="Csnk2a1",]
# add the gene activity matrix to the Seurat object as a new assay
combined [['RNA']] <- CreateAssayObject(counts = gene.activities)

combined <- NormalizeData(
  object = combined ,
  assay = 'RNA',
  normalization.method = 'LogNormalize',
  scale.factor = median(combined $nCount_RNA)
) %>% ScaleData(assay = 'RNA')

######motif analysis
library(JASPAR2020)
library(TFBSTools)
library(BSgenome.Mmusculus.UCSC.mm10)
library(patchwork)
set.seed(1234)
library(rtracklayer)
DefaultAssay(neoThy) <- "ATAC"
pfm <- getMatrixSet(
  x = JASPAR2020,
  opts = list(species = 9606, all_versions = FALSE)
)
combined <- AddMotifs(
  object = combined ,
  genome = BSgenome.Mmusculus.UCSC.mm10,
  pfm = pfm
)

combined<-RunChromVAR(
  object = combined,
  genome = BSgenome.Mmusculus.UCSC.mm10,
  assay = "ATAC",
  new.assay.name = "chromvar",
)

pwm <- getMatrixSet(
  x = JASPAR2020,
  opts = list(species = 9606, all_versions = FALSE)
)
combined<- AddMotifs(combined, genome = BSgenome.Mmusculus.UCSC.mm10, pfm = pwm)
test4 <- Footprint(
   object = combined,
   motif.name = c("ZBTB14","EGR3","RORA"),
   genome = BSgenome.Mmusculus.UCSC.mm10,
 )
Computing Tn5 insertion bias
Extracting reads in requested region
Extracting reads in requested region
**Error in rbindlist(l, use.names, fill, idcol) : 
  Item 2 has 6 columns, inconsistent with item 1 which has 7 columns. To fill missing columns use fill=TRUE.**

**Here show the sessionInfo() in formation.**
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Matrix_1.3-2                       BiocParallel_1.24.1                RColorBrewer_1.1-2                
 [4] patchwork_1.1.1                    BSgenome.Mmusculus.UCSC.mm10_1.4.0 BSgenome_1.58.0                   
 [7] rtracklayer_1.50.0                 Biostrings_2.58.0                  XVector_0.30.0                    
[10] TFBSTools_1.28.0                   JASPAR2020_0.99.10                 ggrepel_0.9.1                     
[13] cicero_1.3.4.11                    Gviz_1.34.1                        shiny_1.6.0                       
[16] SeuratWrappers_0.3.0               monocle3_1.0.0                     SingleCellExperiment_1.12.0       
[19] SummarizedExperiment_1.20.0        MatrixGenerics_1.2.1               matrixStats_0.58.0                
[22] Biobase_2.50.0                     future_1.21.0                      GenomicRanges_1.42.0              
[25] GenomeInfoDb_1.26.4                IRanges_2.24.1                     S4Vectors_0.28.1                  
[28] BiocGenerics_0.36.0                SeuratObject_4.0.0                 Seurat_4.0.1                      
[31] Signac_1.1.1                       cowplot_1.1.1                      tidyr_1.1.3                       
[34] dplyr_1.0.5                        ggplot2_3.3.3                      ggrastr_0.2.3                     

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.3              SnowballC_0.7.0             scattermore_0.7             GGally_2.1.1               
  [5] R.methodsS3_1.8.1           bit64_4.0.5                 knitr_1.31                  R.utils_2.10.1             
  [9] irlba_2.3.3                 DelayedArray_0.16.3         data.table_1.14.0           rpart_4.1-15               
 [13] KEGGREST_1.30.1             RCurl_1.98-1.3              AnnotationFilter_1.14.0     generics_0.1.0             
 [17] GenomicFeatures_1.42.2      RSQLite_2.2.4               RANN_2.6.1                  VGAM_1.1-5                 
 [21] bit_4.0.4                   spatstat.data_2.1-0         xml2_1.3.2                  httpuv_1.5.5               
 [25] assertthat_0.2.1            DirichletMultinomial_1.32.0 viridis_0.5.1               xfun_0.22                  
 [29] hms_1.0.0                   promises_1.2.0.1            fansi_0.4.2                 progress_1.2.2             
 [33] caTools_1.18.1              dbplyr_2.1.0                igraph_1.2.6                DBI_1.1.1                  
 [37] htmlwidgets_1.5.3           reshape_0.8.8               spatstat.geom_2.0-1         purrr_0.3.4                
 [41] ellipsis_0.3.1              backports_1.2.1             annotate_1.68.0             biomaRt_2.46.3             
 [45] deldir_0.2-10               vctrs_0.3.6                 remotes_2.2.0               ensembldb_2.14.0           
 [49] ROCR_1.0-11                 abind_1.4-5                 cachem_1.0.4                withr_2.4.1                
 [53] ggforce_0.3.3               checkmate_2.0.0             sctransform_0.3.2           GenomicAlignments_1.26.0   
 [57] prettyunits_1.1.1           goftest_1.2-2               cluster_2.1.1               lazyeval_0.2.2             
 [61] seqLogo_1.56.0              crayon_1.4.1                pkgconfig_2.0.3             tweenr_1.0.2               
 [65] nlme_3.1-152                vipor_0.4.5                 ProtGenerics_1.22.0         nnet_7.3-15                
 [69] rlang_0.4.10                globals_0.14.0              lifecycle_1.0.0             miniUI_0.1.1.1             
 [73] BiocFileCache_1.14.0        rsvd_1.0.3                  dichromat_2.0-0             polyclip_1.10-0            
 [77] lmtest_0.9-38               graph_1.68.0                ggseqlogo_0.1               zoo_1.8-9                  
 [81] base64enc_0.1-3             beeswarm_0.3.1              ggridges_0.5.3              png_0.1-7                  
 [85] viridisLite_0.3.0           bitops_1.0-6                R.oo_1.24.0                 KernSmooth_2.23-18         
 [89] blob_1.2.1                  stringr_1.4.0               parallelly_1.24.0           readr_1.4.0                
 [93] jpeg_0.1-8.1                CNEr_1.26.0                 scales_1.1.1                memoise_2.0.0              
 [97] magrittr_2.0.1              plyr_1.8.6                  ica_1.0-2                   zlibbioc_1.36.0            
[101] compiler_4.0.3              tinytex_0.30                fitdistrplus_1.1-3          Rsamtools_2.6.0            
[105] cli_2.3.1                   listenv_0.8.0               pbapply_1.4-3               htmlTable_2.1.0            
[109] Formula_1.2-4               MASS_7.3-53.1               mgcv_1.8-34                 tidyselect_1.1.0           
[113] stringi_1.5.3               askpass_1.1                 latticeExtra_0.6-29         VariantAnnotation_1.36.0   
[117] fastmatch_1.1-0             tools_4.0.3                 future.apply_1.7.0          rstudioapi_0.13            
[121] TFMPvalue_0.0.8             foreign_0.8-81              lsa_0.73.2                  gridExtra_2.3              
[125] farver_2.1.0                Rtsne_0.15                  digest_0.6.27               BiocManager_1.30.10        
[129] pracma_2.3.3                Rcpp_1.0.6                  later_1.1.0.1               RcppAnnoy_0.0.18           
[133] OrganismDbi_1.32.0          httr_1.4.2                  AnnotationDbi_1.52.0        ggbio_1.38.0               
[137] biovizBase_1.38.0           colorspace_2.0-0            XML_3.99-0.6                tensor_1.5                 
[141] reticulate_1.18             splines_4.0.3               uwot_0.1.10                 RBGL_1.66.0                
[145] RcppRoll_0.3.0              spatstat.utils_2.1-0        plotly_4.9.3                xtable_1.8-4               
[149] poweRlaw_0.70.6             jsonlite_1.7.2              R6_2.5.0                    Hmisc_4.5-0                
[153] pillar_1.5.1                htmltools_0.5.1.1           mime_0.10                   glue_1.4.2                 
[157] fastmap_1.1.0               codetools_0.2-18            utf8_1.2.1                  lattice_0.20-41            
[161] spatstat.sparse_2.0-0       tibble_3.1.0                curl_4.3                    ggbeeswarm_0.6.0           
[165] leiden_0.3.7                gtools_3.8.2                GO.db_3.12.1                openssl_1.4.3              
[169] survival_3.2-10             munsell_0.5.0               GenomeInfoDbData_1.2.4      reshape2_1.4.4             
[173] gtable_0.3.0                spatstat.core_2.0-0
timoast commented 3 years ago

We just released a new version of Signac (1.2.0), can you try updating and see if you still have this error? Can you also see if you get the error when running on one of the un-merged objects, eg V4?

summer-tao commented 3 years ago

We just released a new version of Signac (1.2.0), can you try updating and see if you still have this error? Can you also see if you get the error when running on one of the un-merged objects, eg V4?

Dear Tim, Thanks for your suggestion. I have try the V4 and V6, for V6, everything is fine. But for V4, there is the same error: Computing Tn5 insertion bias Extracting reads in requested region Extracting reads in requested region Error in rbindlist(l, use.names, fill, idcol) : Item 2 has 7 columns, inconsistent with item 1 which has 6 columns. To fill missing columns use fill=TRUE.

So here I paste the structure of V4, in case you can find something I missed. Formal class 'Seurat' [package "SeuratObject"] with 13 slots ..@ assays :List of 2 .. ..$ ATAC :Formal class 'ChromatinAssay' [package "Signac"] with 16 slots .. .. .. ..@ ranges :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 21 levels "chr1","chr2",..: 1 2 3 4 5 6 7 8 9 10 ... .. .. .. .. .. .. .. ..@ lengths : int [1:21] 13313 15057 9508 11362 12269 10659 11080 8825 11131 9983 ... .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:190719] 3551152 3670444 4332396 4414852 4416678 4432436 4433561 4468393 4470233 4478583 ... .. .. .. .. .. .. .. ..@ width : int [1:190719] 286 872 500 133 471 210 354 1325 303 274 ... .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","": 3 .. .. .. .. .. .. .. ..@ lengths : int 190719 .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:21] "chr1" "chr2" "chr3" "chr4" ... .. .. .. .. .. .. .. ..@ seqlengths : int [1:21] NA NA NA NA NA NA NA NA NA NA ... .. .. .. .. .. .. .. ..@ is_circular: logi [1:21] NA NA NA NA NA NA ... .. .. .. .. .. .. .. ..@ genome : chr [1:21] NA NA NA NA ... .. .. .. .. .. ..@ elementMetadata:Formal class 'DFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 190719 .. .. .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ motifs :Formal class 'Motif' [package "Signac"] with 5 slots .. .. .. .. .. ..@ data :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots .. .. .. .. .. .. .. ..@ i : int [1:13656132] 42 51 53 55 58 68 81 116 130 133 ... .. .. .. .. .. .. .. ..@ p : int [1:634] 0 21800 34252 63002 97362 119101 140894 151642 166518 190737 ... .. .. .. .. .. .. .. ..@ Dim : int [1:2] 190719 633 .. .. .. .. .. .. .. ..@ Dimnames:List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:190719] "chr1-3551152-3551437" "chr1-3670444-3671315" "chr1-4332396-4332895" "chr1-4414852-4414984" ... .. .. .. .. .. .. .. .. ..$ : chr [1:633] "MA0030.1" "MA0031.1" "MA0051.1" "MA0057.1" ... .. .. .. .. .. .. .. ..@ x : num [1:13656132] 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. .. .. .. ..@ factors : list() .. .. .. .. .. ..@ pwm :List of 633 .. .. .. .. .. .. ..$ MA0030.1: int [1:4, 1:14] 1 10 7 9 10 7 5 5 17 4 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0031.1: int [1:4, 1:8] 1 1 17 1 0 0 0 20 19 1 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0051.1: int [1:4, 1:18] 0 4 7 1 2 0 10 0 12 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0057.1: int [1:4, 1:10] 1 4 7 4 2 0 7 7 15 1 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0059.1: int [1:4, 1:11] 7 1 9 4 15 1 4 1 2 9 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0066.1: int [1:4, 1:20] 3 8 14 3 3 0 0 25 19 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0069.1: int [1:4, 1:14] 2 4 4 33 2 2 0 39 4 26 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0070.1: int [1:4, 1:12] 5 6 2 5 3 9 3 3 16 1 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0071.1: int [1:4, 1:10] 15 1 2 7 9 1 0 15 6 12 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0072.1: int [1:4, 1:14] 9 8 8 11 17 2 7 10 15 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0073.1: int [1:4, 1:20] 3 8 0 0 1 10 0 0 3 8 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0074.1: int [1:4, 1:15] 3 0 7 0 0 0 10 0 0 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0077.1: int [1:4, 1:9] 3 55 9 9 8 38 6 24 71 1 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0084.1: int [1:4, 1:9] 5 5 10 8 8 3 4 13 15 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0091.1: int [1:4, 1:12] 13 14 8 9 9 10 20 5 39 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0101.1: int [1:4, 1:10] 0 5 8 4 0 1 15 1 1 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0107.1: int [1:4, 1:10] 0 4 11 3 0 0 17 1 0 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0115.1: int [1:4, 1:17] 17 5 0 3 17 1 5 2 20 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0119.1: int [1:4, 1:14] 0 0 0 16 0 0 16 0 0 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0130.1: int [1:4, 1:6] 7 6 3 0 3 2 0 11 0 16 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0139.1: int [1:4, 1:19] 87 291 76 459 167 145 414 187 281 49 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0149.1: int [1:4, 1:18] 0 0 105 0 2 0 103 0 104 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0138.2: int [1:4, 1:21] 211 174 366 840 58 269 146 1124 76 1366 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0152.1: int [1:4, 1:7] 3 1 2 20 1 2 2 21 1 1 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0155.1: int [1:4, 1:12] 1 0 4 19 0 0 20 4 0 8 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0159.1: int [1:4, 1:17] 12 0 11 0 0 0 23 0 1 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0160.1: int [1:4, 1:8] 8 1 3 1 13 0 1 0 0 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0163.1: int [1:4, 1:14] 0 0 18 0 3 0 14 1 0 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0259.1: int [1:4, 1:8] 27 28 49 0 10 29 34 31 78 2 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0468.1: int [1:4, 1:11] 7297 2495 979 27446 37001 0 1216 0 38217 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0476.1: int [1:4, 1:11] 7879 712 9686 11119 7475 10177 10841 903 0 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0478.1: int [1:4, 1:11] 833 994 2086 1405 1525 592 2707 494 2861 55 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0479.1: int [1:4, 1:11] 939 2840 1490 2942 1578 2333 2137 2163 973 3261 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0488.1: int [1:4, 1:13] 8141 2792 4894 5141 7116 2938 4985 5929 6496 1903 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0489.1: int [1:4, 1:14] 4852 1250 2818 2036 3927 1324 4110 1595 3726 1127 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0492.1: int [1:4, 1:15] 11448 4326 7996 9861 13436 3228 8721 8246 11261 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.. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0527.1: int [1:4, 1:15] 82 256 146 221 6 66 32 601 28 659 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0076.2: int [1:4, 1:11] 298 1458 886 785 391 1905 570 561 2034 145 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0258.2: int [1:4, 1:15] 5410 96 2563 174 429 0 7170 644 59 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0050.2: int [1:4, 1:21] 316 320 266 460 251 284 251 576 173 324 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0137.3: int [1:4, 1:11] 366 731 785 1747 0 52 0 3577 0 6 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0144.2: int [1:4, 1:11] 1936 8571 3801 7312 708 0 0 20912 250 346 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0140.2: int [1:4, 1:18] 1114 2038 967 836 206 807 159 3783 318 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0095.2: int [1:4, 1:12] 1126 4583 801 661 6975 0 181 15 6741 99 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0593.1: int [1:4, 1:11] 330 113 190 133 340 7 142 277 160 0 ... .. 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"A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0610.1: int [1:4, 1:11] 453 240 154 154 539 123 123 216 106 22 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0613.1: int [1:4, 1:8] 374 1 623 1 1 1 1 997 997 1 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0618.1: int [1:4, 1:8] 217 131 174 478 0 49 0 951 999 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0625.1: int [1:4, 1:10] 421 93 139 348 179 181 168 472 117 40 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0628.1: int [1:4, 1:10] 507 193 211 89 151 351 145 353 32 10 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0630.1: int [1:4, 1:8] 179 301 162 357 74 30 9 886 852 48 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0634.1: int [1:4, 1:10] 1251 2174 1062 3390 987 3402 1150 2337 794 3367 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0635.1: int [1:4, 1:10] 3318 3450 4374 1713 3328 4078 1756 3693 643 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0636.1: int [1:4, 1:10] 2894 1046 5574 59 98 17 1831 5574 2 5574 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0637.1: int [1:4, 1:15] 685 5580 3 734 100 5580 4 144 2 5580 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0638.1: int [1:4, 1:14] 79 78 107 50 32 78 75 284 20 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0639.1: int [1:4, 1:12] 1552 1714 1903 1930 3706 1130 3393 93 5 4 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0641.1: int [1:4, 1:12] 598 109 160 192 705 73 15 149 198 930 ... .. .. .. .. .. .. .. ..- attr(, 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"G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0157.2: int [1:4, 1:8] 21 0 532 0 0 0 13 532 532 16 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0646.1: int [1:4, 1:11] 2522 8553 5154 5210 21439 1811 4010 261 161 154 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0647.1: int [1:4, 1:12] 1345 472 247 427 2491 109 409 418 2491 3 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0648.1: int [1:4, 1:10] 1249 1912 2039 882 955 2885 553 1688 0 54 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0649.1: int [1:4, 1:10] 107 99 1800 101 651 305 620 224 84 1800 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0131.2: int [1:4, 1:12] 23 340 106 100 285 131 113 53 276 45 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0046.2: int [1:4, 1:15] 5209 2441 3490 3009 6981 415 7168 636 376 1060 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0153.2: int [1:4, 1:13] 1528 1030 30839 1628 541 2552 1434 30839 5730 3466 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0651.1: int [1:4, 1:11] 683 260 1110 406 1040 479 2460 0 38 41 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0486.2: int [1:4, 1:13] 64 18 25 1455 11 4 17 1455 9 1455 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0652.1: int [1:4, 1:14] 1309 1996 571 2002 63 5878 19 884 3 0 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0653.1: int [1:4, 1:15] 3467 52 43 110 2392 498 204 1076 49 3467 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0654.1: int [1:4, 1:8] 318 863 364 520 10 1003 0 1061 2065 48 ... .. .. .. .. 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.. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0660.1: int [1:4, 1:12] 1385 72 1766 505 18 3150 0 12 0 25 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0661.1: int [1:4, 1:10] 906 704 986 405 150 1637 1363 115 64 406 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0662.1: int [1:4, 1:10] 6774 6037 6646 7585 3981 9030 5461 8570 2635 11639 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. ..$ MA0663.1: int [1:4, 1:10] 177 4 110 41 0 17 61 322 3 251 ... .. .. .. .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. .. .. .. ..$ : chr [1:4] "A" "C" "G" "T" .. .. .. .. .. .. .. .. ..$ : NULL .. .. .. .. .. .. .. [list output truncated] .. .. .. .. .. ..@ motif.names:List of 633 .. .. .. .. .. .. ..$ MA0030.1: chr "FOXF2" .. .. .. .. .. .. ..$ MA0031.1: chr "FOXD1" .. .. .. .. .. .. ..$ MA0051.1: chr "IRF2" .. .. .. .. .. .. ..$ MA0057.1: chr "MZF1(var.2)" .. .. .. .. .. .. ..$ MA0059.1: chr "MAX::MYC" .. .. .. .. .. .. ..$ MA0066.1: chr "PPARG" .. .. .. .. .. .. ..$ MA0069.1: chr "PAX6" .. .. .. .. .. .. ..$ MA0070.1: chr "PBX1" .. .. .. .. .. .. ..$ MA0071.1: chr "RORA" .. .. .. .. .. .. ..$ MA0072.1: chr "RORA(var.2)" .. .. .. .. .. .. ..$ MA0073.1: chr "RREB1" .. .. .. .. .. .. ..$ MA0074.1: chr "RXRA::VDR" .. .. .. .. .. .. ..$ MA0077.1: chr "SOX9" .. .. .. .. .. .. ..$ MA0084.1: chr "SRY" .. .. .. .. .. .. ..$ MA0091.1: chr "TAL1::TCF3" .. .. .. .. .. .. ..$ MA0101.1: chr "REL" .. .. .. .. .. .. ..$ MA0107.1: chr "RELA" .. .. .. .. .. .. ..$ MA0115.1: chr "NR1H2::RXRA" .. .. .. .. .. .. ..$ MA0119.1: chr "NFIC::TLX1" .. .. .. .. .. .. ..$ MA0130.1: chr "ZNF354C" .. .. .. .. .. .. ..$ MA0139.1: chr "CTCF" .. .. .. .. .. .. ..$ MA0149.1: chr "EWSR1-FLI1" .. .. .. .. .. .. ..$ MA0138.2: chr "REST" .. .. .. .. .. .. ..$ MA0152.1: chr "NFATC2" .. .. .. .. .. .. ..$ MA0155.1: chr "INSM1" .. .. .. .. .. .. ..$ MA0159.1: chr "RARA::RXRA" .. .. .. .. .. .. ..$ MA0160.1: chr "NR4A2" .. .. .. .. .. .. ..$ MA0163.1: chr "PLAG1" .. .. .. .. .. .. ..$ MA0259.1: chr "ARNT::HIF1A" .. .. .. .. .. .. ..$ MA0468.1: chr "DUX4" .. .. .. .. .. .. ..$ MA0476.1: chr "FOS" .. .. .. .. .. .. ..$ MA0478.1: chr "FOSL2" .. .. .. .. .. .. ..$ MA0479.1: chr "FOXH1" .. .. .. .. .. .. ..$ MA0488.1: chr "JUN" .. .. .. .. .. .. ..$ MA0489.1: chr "JUN(var.2)" .. .. .. .. .. .. ..$ MA0492.1: chr "JUND(var.2)" .. .. .. .. .. .. ..$ MA0497.1: chr "MEF2C" .. .. .. .. .. .. ..$ MA0501.1: chr "MAF::NFE2" .. .. .. .. .. .. ..$ MA0504.1: chr "NR2C2" .. .. .. .. .. .. ..$ MA0506.1: chr "NRF1" .. .. .. .. .. .. ..$ MA0507.1: chr "POU2F2" .. .. .. .. .. .. ..$ MA0513.1: chr "SMAD2::SMAD3::SMAD4" .. .. .. .. .. .. ..$ MA0517.1: chr "STAT1::STAT2" .. .. .. .. .. .. ..$ MA0523.1: chr "TCF7L2" .. .. .. .. .. .. ..$ MA0527.1: chr "ZBTB33" .. .. .. .. .. .. ..$ MA0076.2: chr "ELK4" .. .. .. .. .. .. ..$ MA0258.2: chr "ESR2" .. .. .. .. .. .. ..$ MA0050.2: chr "IRF1" .. .. .. .. .. .. ..$ MA0137.3: chr "STAT1" .. .. .. .. .. .. ..$ MA0144.2: chr "STAT3" .. .. .. .. .. .. ..$ MA0140.2: chr "GATA1::TAL1" .. .. .. .. .. .. ..$ MA0095.2: chr "YY1" .. .. .. .. .. .. ..$ MA0593.1: chr "FOXP2" .. .. .. .. .. .. ..$ MA0595.1: chr "SREBF1" .. .. .. .. .. .. ..$ MA0596.1: chr "SREBF2" .. .. .. .. .. .. ..$ MA0597.1: chr "THAP1" .. .. .. .. .. .. ..$ MA0599.1: chr "KLF5" .. .. .. .. .. .. ..$ MA0610.1: chr "DMRT3" .. .. .. .. .. .. ..$ MA0613.1: chr "FOXG1" .. .. .. .. .. .. ..$ MA0618.1: chr "LBX1" .. .. .. .. .. .. ..$ MA0625.1: chr "NFATC3" .. .. .. .. .. .. ..$ MA0628.1: chr "POU6F1" .. .. .. .. .. .. ..$ MA0630.1: chr "SHOX" .. .. .. .. .. .. ..$ MA0634.1: chr "ALX3" .. .. .. .. .. .. ..$ MA0635.1: chr "BARHL2" .. .. .. .. .. .. ..$ MA0636.1: chr "BHLHE41" .. .. .. .. .. .. ..$ MA0637.1: chr "CENPB" .. .. .. .. .. .. ..$ MA0638.1: chr "CREB3" .. .. .. .. .. .. ..$ MA0639.1: chr "DBP" .. .. .. .. .. .. ..$ MA0641.1: chr "ELF4" .. .. .. .. .. .. ..$ MA0136.2: chr "ELF5" .. .. .. .. .. .. ..$ MA0027.2: chr "EN1" .. .. .. .. .. .. ..$ MA0642.1: chr "EN2" .. .. .. .. .. .. ..$ MA0644.1: chr "ESX1" .. .. .. .. .. .. ..$ MA0645.1: chr "ETV6" .. .. .. .. .. .. ..$ MA0475.2: chr "FLI1" .. .. .. .. .. .. ..$ MA0042.2: chr "FOXI1" .. .. .. .. .. .. ..$ MA0033.2: chr "FOXL1" .. .. .. .. .. .. ..$ MA0157.2: chr "FOXO3" .. .. .. .. .. .. ..$ MA0646.1: chr "GCM1" .. .. .. .. .. .. ..$ MA0647.1: chr "GRHL1" .. .. .. .. .. .. ..$ MA0648.1: chr "GSC" .. .. .. .. .. .. ..$ MA0649.1: chr "HEY2" .. .. .. .. .. .. ..$ MA0131.2: chr "HINFP" .. .. .. .. .. .. ..$ MA0046.2: chr "HNF1A" .. .. .. .. .. .. ..$ MA0153.2: chr "HNF1B" .. .. .. .. .. .. ..$ MA0651.1: chr "HOXC11" .. .. .. .. .. .. ..$ MA0486.2: chr "HSF1" .. .. .. .. .. .. ..$ MA0652.1: chr "IRF8" .. .. .. .. .. .. ..$ MA0653.1: chr "IRF9" .. .. .. .. .. .. ..$ MA0654.1: chr "ISX" .. .. .. .. .. .. ..$ MA0655.1: chr "JDP2" .. .. .. .. .. .. ..$ MA0656.1: chr "JDP2(var.2)" .. .. .. .. .. .. ..$ MA0657.1: chr "KLF13" .. .. .. .. .. .. ..$ MA0658.1: chr "LHX6" .. .. .. .. .. .. ..$ MA0660.1: chr "MEF2B" .. .. .. .. .. .. ..$ MA0661.1: chr "MEOX1" .. .. .. .. .. .. ..$ MA0662.1: chr "MIXL1" .. .. .. .. .. .. ..$ MA0663.1: chr "MLX" .. .. .. .. .. .. .. [list output truncated] .. .. .. .. .. ..@ positions :Formal class 'CompressedGRangesList' [package "GenomicRanges"] with 5 slots .. .. .. .. .. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots .. .. .. .. .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. .. .. .. .. ..@ values : Factor w/ 21 levels "chr1","chr2",..: 1 2 3 4 5 6 7 8 9 10 ... .. .. .. .. .. .. .. .. .. .. .. ..@ lengths : int [1:13134] 1824 1945 1430 1464 1585 1438 1449 1106 1493 1420 ... .. .. .. .. .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. .. .. .. .. ..@ start : int [1:21502782] 5082749 6144175 6213990 6226637 6261197 6383561 6519025 7543848 9697167 9703461 ... .. .. .. .. .. .. .. .. .. .. .. ..@ width : int [1:21502782] 14 14 14 14 14 14 14 14 14 14 ... .. .. .. .. .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","": 1 2 1 2 1 2 1 2 1 2 ... .. .. .. .. .. .. .. .. .. .. .. ..@ lengths : int [1:9901842] 2 3 1 1 5 2 2 1 1 2 ... .. .. .. .. .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. .. .. .. .. ..@ seqnames : chr [1:21] "chr1" "chr2" "chr3" "chr4" ... .. .. .. .. .. .. .. .. .. .. .. ..@ seqlengths : int [1:21] NA NA NA NA NA NA NA NA NA NA ... .. .. .. .. .. .. .. .. .. .. .. ..@ is_circular: logi [1:21] NA NA NA NA NA NA ... .. .. .. .. .. .. .. .. .. .. .. ..@ genome : chr [1:21] NA NA NA NA ... .. .. .. .. .. .. .. .. .. ..@ elementMetadata:Formal class 'DFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. .. .. .. .. ..@ nrows : int 21502782 .. .. .. .. .. .. .. .. .. .. .. ..@ listData :List of 1 .. .. .. .. .. .. .. .. .. .. .. .. ..$ score: num [1:21502782] 15.7 12.7 12.2 13.6 14.7 ... .. .. .. .. .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. .. .. ..@ elementMetadata:Formal class 'DFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. .. .. ..@ nrows : int 633 .. .. .. .. .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. .. .. ..@ elementType : chr "GRanges" .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots .. .. .. .. .. .. .. .. .. ..@ end : int [1:633] 25510 39078 76357 126028 155526 184659 196378 214182 242571 262890 ... .. .. .. .. .. .. .. .. .. ..@ NAMES : chr [1:633] "MA0030.1" "MA0031.1" "MA0051.1" "MA0057.1" ... .. .. .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ meta.data :'data.frame': 0 obs. of 0 variables .. .. .. ..@ fragments :List of 2 .. .. .. .. ..$ :Formal class 'Fragment' [package "Signac"] with 3 slots .. .. .. .. .. .. ..@ path : chr "/home/large/Tao/ATAC_mouse/2021_037582_1/Thy_Vg4/outs/fragments.tsv.gz" .. .. .. .. .. .. ..@ hash : chr [1:2] "f30099384bac642ed89d8982cf320667" "ac47024051f4ddd7991e2b29a27e1f70" .. .. .. .. .. .. ..@ cells: Named chr(0) .. .. .. .. .. .. .. ..- attr(, "names")= chr(0) .. .. .. .. ..$ :Formal class 'Fragment' [package "Signac"] with 3 slots .. .. .. .. .. .. ..@ path : chr "/home/large/Tao/neonatal-Thymus/rawData/neoThy_Vg4/outs/fragments.tsv.gz" .. .. .. .. .. .. ..@ hash : chr [1:2] "f006a1537a82287b65218356c41460b9" "0e904697980c34b35098dd0bd7926531" .. .. .. .. .. .. ..@ cells: Named chr [1:1117] "AAACGAAAGCACGTAG-1" "AAACGAAGTTCAGTTG-1" "AAACGAAGTTTCACCC-1" "AAACTCGCAAACTACC-1" ... .. .. .. .. .. .. .. ..- attr(, "names")= chr [1:1117] "neoTV4_AAACGAAAGCACGTAG-1" "neoTV4_AAACGAAGTTCAGTTG-1" "neoTV4_AAACGAAGTTTCACCC-1" "neoTV4_AAACTCGCAAACTACC-1" ... .. .. .. .. .. .. .. ..- attr(, ".match.hash")=Class 'match.hash' .. .. .. ..@ seqinfo : NULL .. .. .. ..@ annotation :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 22 levels "chr3","chrX",..: 1 2 3 4 5 6 7 8 9 10 ... .. .. .. .. .. .. .. ..@ lengths : int [1:22] 83099 68561 56688 128222 149106 89406 49376 121281 98969 10906 ... .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int [1:1763965] 3508030 3634150 3638059 3638059 3641223 3641223 3642964 3642964 3644536 3644536 ... .. .. .. .. .. .. .. ..@ width : int [1:1763965] 303 198 172 172 95 95 107 107 156 156 ... .. .. .. .. .. .. .. ..@ NAMES : chr [1:1763965] "ENSMUSE00001236884" "ENSMUSE00000676606" "ENSMUSE00001345708" "ENSMUSE00001345708" ... .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","": 1 2 1 2 1 2 1 2 1 2 ... .. .. .. .. .. .. .. ..@ lengths : int [1:65507] 69 30 1 6 28 37 15 87 16 1 ... .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr [1:22] "chr3" "chrX" "chr16" "chr7" ... .. .. .. .. .. .. .. ..@ seqlengths : int [1:22] 160039680 171031299 98207768 145441459 122082543 149736546 120421639 156508116 124595110 91744698 ... .. .. .. .. .. .. .. ..@ is_circular: logi [1:22] FALSE FALSE FALSE FALSE FALSE FALSE ... .. .. .. .. .. .. .. ..@ genome : chr [1:22] "mm10" "mm10" "mm10" "mm10" ... .. .. .. .. .. ..@ elementMetadata:Formal class 'DFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 1763965 .. .. .. .. .. .. .. ..@ listData :List of 5 .. .. .. .. .. .. .. .. ..$ tx_id : chr [1:1763965] "ENSMUST00000108393" "ENSMUST00000108394" "ENSMUST00000108393" "ENSMUST00000108394" ... .. .. .. .. .. .. .. .. ..$ gene_name : chr [1:1763965] "Hnf4g" "Hnf4g" "Hnf4g" "Hnf4g" ... .. .. .. .. .. .. .. .. ..$ gene_id : chr [1:1763965] "ENSMUSG00000017688" "ENSMUSG00000017688" "ENSMUSG00000017688" "ENSMUSG00000017688" ... .. .. .. .. .. .. .. .. ..$ gene_biotype: chr [1:1763965] "protein_coding" "protein_coding" "protein_coding" "protein_coding" ... .. .. .. .. .. .. .. .. ..$ type : Factor w/ 4 levels "cds","exon","gap",..: 2 2 2 2 2 2 2 2 2 2 ... .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ bias : NULL .. .. .. ..@ positionEnrichment:List of 1 .. .. .. .. ..$ TSS:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots .. .. .. .. .. .. ..@ i : int [1:1882525] 0 3 5 6 7 8 9 11 12 13 ... .. .. .. .. .. .. ..@ p : int [1:2002] 0 512 1034 1640 2194 2790 3401 3996 4582 5170 ... .. .. .. .. .. .. ..@ Dim : int [1:2] 1117 2001 .. .. .. .. .. .. ..@ Dimnames:List of 2 .. .. .. .. .. .. .. ..$ : chr [1:1117] "neoTV4_AAACGAAAGCACGTAG-1" "neoTV4_AAACGAAGTTCAGTTG-1" "neoTV4_AAACGAAGTTTCACCC-1" "neoTV4_AAACTCGCAAACTACC-1" ... .. .. .. .. .. .. .. ..$ : chr [1:2001] "-999" "-998" "-997" "-996" ... .. .. .. .. .. .. ..@ x : num [1:1882525] 0.755 0.738 1.227 0.791 0.513 ... .. .. .. .. .. .. ..@ factors : list() .. .. .. ..@ links :Formal class 'GRanges' [package "GenomicRanges"] with 7 slots .. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 0 levels: .. .. .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. .. ..@ start : int(0) .. .. .. .. .. .. .. ..@ width : int(0) .. .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots .. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","": .. .. .. .. .. .. .. ..@ lengths : int(0) .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots .. .. .. .. .. .. .. ..@ seqnames : chr(0) .. .. .. .. .. .. .. ..@ seqlengths : int(0) .. .. .. .. .. .. .. ..@ is_circular: logi(0) .. .. .. .. .. .. .. ..@ genome : chr(0) .. .. .. .. .. ..@ elementMetadata:Formal class 'DFrame' [package "S4Vectors"] with 6 slots .. .. .. .. .. .. .. ..@ rownames : NULL .. .. .. .. .. .. .. ..@ nrows : int 0 .. .. .. .. .. .. .. ..@ listData : Named list() .. .. .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. .. ..@ metadata : list() .. .. .. ..@ counts :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots .. .. .. .. .. ..@ i : int [1:9684224] 53 89 93 103 107 122 143 211 241 282 ... .. .. .. .. .. ..@ p : int [1:1118] 0 9289 21679 28672 38079 45039 54986 64120 77428 92876 ... .. .. .. .. .. ..@ Dim : int [1:2] 190719 1117 .. .. .. .. .. ..@ Dimnames:List of 2 .. .. .. .. .. .. ..$ : chr [1:190719] "chr1-3551152-3551437" "chr1-3670444-3671315" "chr1-4332396-4332895" "chr1-4414852-4414984" ... .. .. .. .. .. .. ..$ : chr [1:1117] "neoTV4_AAACGAAAGCACGTAG-1" "neoTV4_AAACGAAGTTCAGTTG-1" "neoTV4_AAACGAAGTTTCACCC-1" "neoTV4_AAACTCGCAAACTACC-1" ... .. .. .. .. .. ..@ x : num [1:9684224] 1 3 1 1 2 1 1 1 1 1 ... .. .. .. .. .. ..@ factors : list() .. .. .. ..@ data :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots .. .. .. .. .. ..@ i : int [1:9684224] 53 89 93 103 107 122 143 211 241 282 ... .. .. .. .. .. ..@ p : int [1:1118] 0 9289 21679 28672 38079 45039 54986 64120 77428 92876 ... .. .. .. .. .. ..@ Dim : int [1:2] 190719 1117 .. .. .. .. .. ..@ Dimnames:List of 2 .. .. .. .. .. .. ..$ : chr [1:190719] "chr1-3551152-3551437" "chr1-3670444-3671315" "chr1-4332396-4332895" "chr1-4414852-4414984" ... .. .. .. .. .. .. ..$ : chr [1:1117] "neoTV4_AAACGAAAGCACGTAG-1" "neoTV4_AAACGAAGTTCAGTTG-1" "neoTV4_AAACGAAGTTTCACCC-1" "neoTV4AAACTCGCAAACTACC-1" ... .. .. .. .. .. ..@ x : num [1:9684224] 0.729 1.185 3.001 1.61 0.915 ... .. .. .. .. .. ..@ factors : list() .. .. .. ..@ scale.data : num[0 , 0 ] .. .. .. ..@ key : chr "ATAC" .. .. .. ..@ assay.orig : NULL .. .. .. ..@ var.features : chr [1:183616] "chr17-39842748-39849073" "chr9-57070736-57078434" "chr9-124422275-124426770" "chr8-11554444-11560644" ... .. .. .. ..@ meta.features :'data.frame': 190719 obs. of 20 variables: .. .. .. .. ..$ count : num [1:190719] 3 19 22 6 13 3 3 22 6 4 ... .. .. .. .. ..$ percentile : num [1:190719] 0.158 0.584 0.612 0.302 0.502 ... .. .. .. .. ..$ AA : num [1:190719] 22 33 43 7 43 23 39 122 26 21 ... .. .. .. .. ..$ AC : num [1:190719] 14 41 27 13 29 13 16 84 22 13 ... .. .. .. .. ..$ AG : num [1:190719] 31 76 39 10 41 21 24 107 24 23 ... .. .. .. .. ..$ AT : num [1:190719] 19 19 40 10 28 16 23 84 19 12 ... .. .. .. .. ..$ CA : num [1:190719] 29 71 51 19 45 29 26 131 35 20 ... .. .. .. .. ..$ CC : num [1:190719] 9 103 27 9 31 7 17 77 25 17 ... .. .. .. .. ..$ CG : num [1:190719] 2 68 3 0 5 0 1 13 0 6 ... .. .. .. .. ..$ CT : num [1:190719] 16 53 38 9 34 15 35 102 21 26 ... .. .. .. .. ..$ GA : num [1:190719] 18 52 27 9 28 9 24 79 13 19 ... .. .. .. .. ..$ GC : num [1:190719] 17 111 24 6 29 13 17 74 14 18 ... .. .. .. .. ..$ GG : num [1:190719] 16 57 13 6 17 4 17 70 23 9 ... .. .. .. .. ..$ GT : num [1:190719] 19 46 22 4 23 9 12 61 15 11 ... .. .. .. .. ..$ TA : num [1:190719] 17 13 27 5 24 13 13 66 18 10 ... .. .. .. .. ..$ TC : num [1:190719] 16 39 41 9 27 18 28 88 20 21 ... .. .. .. .. ..$ TG : num [1:190719] 21 65 32 9 34 9 28 94 17 18 ... .. .. .. .. ..$ TT : num [1:190719] 19 24 45 7 32 10 33 72 10 29 ... .. .. .. .. ..$ GC.percent : num [1:190719] 44.1 64.3 41.2 46.6 45.2 ... .. .. .. .. ..$ sequence.length: num [1:190719] 286 872 500 133 471 ... .. .. .. ..@ misc : list() .. ..$ bodyPromoterRNA:Formal class 'Assay' [package "SeuratObject"] with 8 slots .. .. .. ..@ counts :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots .. .. .. .. .. ..@ i : int [1:6930170] 2 6 11 14 16 26 33 47 48 49 ... .. .. .. .. .. ..@ p : int [1:1118] 0 6834 14949 20294 27092 32677 39886 46716 55171 64739 ... .. .. .. .. .. ..@ Dim : int [1:2] 21976 1117 .. .. .. .. .. ..@ Dimnames:List of 2 .. .. .. .. .. .. ..$ : chr [1:21976] "Hnf4g" "Zfhx4" "Pex2" "UBC" ... .. .. .. .. .. .. ..$ : chr [1:1117] "neoTV4_AAACGAAAGCACGTAG-1" "neoTV4_AAACGAAGTTCAGTTG-1" "neoTV4_AAACGAAGTTTCACCC-1" "neoTV4_AAACTCGCAAACTACC-1" ... .. .. .. .. .. ..@ x : num [1:6930170] 2 2 1 3 1 1 1 1 1 1 ... .. .. .. .. .. ..@ factors : list() .. .. .. ..@ data :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots .. .. .. .. .. ..@ i : int [1:6930170] 2 6 11 14 16 26 33 47 48 49 ... .. .. .. .. .. ..@ p : int [1:1118] 0 6834 14949 20294 27092 32677 39886 46716 55171 64739 ... .. .. .. .. .. ..@ Dim : int [1:2] 21976 1117 .. .. .. .. .. ..@ Dimnames:List of 2 .. .. .. .. .. .. ..$ : chr [1:21976] "Hnf4g" "Zfhx4" "Pex2" "UBC" ... .. .. .. .. .. .. ..$ : chr [1:1117] "neoTV4_AAACGAAAGCACGTAG-1" "neoTV4_AAACGAAGTTCAGTTG-1" "neoTV4_AAACGAAGTTTCACCC-1" "neoTV4AAACTCGCAAACTACC-1" ... .. .. .. .. .. ..@ x : num [1:6930170] 1.289 1.289 0.839 1.598 0.839 ... .. .. .. .. .. ..@ factors : list() .. .. .. ..@ scale.data : num[0 , 0 ] .. .. .. ..@ key : chr "bodypromoterrna" .. .. .. ..@ assay.orig : NULL .. .. .. ..@ var.features : chr(0) .. .. .. ..@ meta.features:'data.frame': 21976 obs. of 0 variables .. .. .. ..@ misc : list() ..@ meta.data :'data.frame': 1117 obs. of 34 variables: .. ..$ orig.ident : chr [1:1117] "SeuratProject" "SeuratProject" "SeuratProject" "SeuratProject" ... .. ..$ nCount_ATAC : num [1:1117] 11417 15897 8408 12239 7766 ... .. ..$ nFeature_ATAC : int [1:1117] 9289 12390 6993 9407 6960 9947 9134 13308 15448 5001 ... .. ..$ total : int [1:1117] 25333 34936 19495 40338 17666 30098 24853 44069 52957 12122 ... .. ..$ duplicate : int [1:1117] 7182 11468 6121 17341 3280 9625 6666 17141 17529 3713 ... .. ..$ chimeric : int [1:1117] 397 487 284 687 247 385 278 696 715 151 ... .. ..$ unmapped : int [1:1117] 732 1106 652 1719 602 1090 841 1212 1623 323 ... .. ..$ lowmapq : int [1:1117] 1588 1744 1101 3069 1354 1905 1391 2198 3416 518 ... .. ..$ mitochondrial : int [1:1117] 0 0 107 39 29 137 137 32 120 10 ... .. ..$ passed_filters : int [1:1117] 15434 20131 11230 17483 12154 16956 15540 22790 29554 7407 ... .. ..$ cell_id : chr [1:1117] "_cell_0" "_cell_5" "_cell_6" "_cell_8" ... .. ..$ is__cell_barcode : int [1:1117] 1 1 1 1 1 1 1 1 1 1 ... .. ..$ TSS_fragments : int [1:1117] 5973 7964 4373 6467 3601 6786 5461 8921 9572 3086 ... .. ..$ DNase_sensitive_region_fragments: int [1:1117] 9726 13664 7437 10817 6661 10939 9543 15333 16924 5126 ... .. ..$ enhancer_region_fragments : int [1:1117] 4745 6934 3620 5208 3815 5195 4973 7569 9300 2375 ... .. ..$ promoter_region_fragments : int [1:1117] 5190 6881 3819 5471 2870 5919 4641 7798 7852 2719 ... .. ..$ on_target_fragments : int [1:1117] 12164 16794 9020 13248 8544 13547 11881 18779 21632 6230 ... .. ..$ blacklist_region_fragments : int [1:1117] 45 113 80 70 47 57 91 62 125 15 ... .. ..$ peak_region_fragments : int [1:1117] 11738 16437 8687 12622 7812 13148 11108 18577 20384 6116 ... .. ..$ peak_region_cutsites : int [1:1117] 22945 32278 17052 24754 15177 25719 21590 36451 39536 11991 ... .. ..$ dataset : chr [1:1117] "neoTV4" "neoTV4" "neoTV4" "neoTV4" ... .. ..$ TSS.enrichment : num [1:1117] 5.42 4.99 7.53 5.83 4.13 ... .. ..$ TSS.percentile : num [1:1117] 0.75 0.6 0.98 0.85 0.18 0.63 0.64 0.83 0.68 0.94 ... .. ..$ high.tss : chr [1:1117] "High" "High" "High" "High" ... .. ..$ nucleosome_signal : num [1:1117] 0.742 0.626 0.786 0.621 0.798 ... .. ..$ nucleosome_percentile : num [1:1117] 0.44 0.13 0.59 0.13 0.63 0.9 0.94 0.11 0.56 0.55 ... .. ..$ nucleosome_group : chr [1:1117] "NS > 0.6" "NS > 0.6" "NS > 0.6" "NS > 0.6" ... .. ..$ pct_reads_in_peaks : num [1:1117] 76.1 81.7 77.4 72.2 64.3 ... .. ..$ blacklist_ratio : num [1:1117] 0.00383 0.00687 0.00921 0.00555 0.00602 ... .. ..$ seurat_clusters : Factor w/ 7 levels "0","1","2","3",..: 2 1 2 2 1 1 1 1 1 2 ... .. ..$ nCount_bodyPromoterRNA : num [1:1117] 11867 15677 8504 13193 8403 ... .. ..$ nFeature_bodyPromoterRNA : int [1:1117] 6834 8115 5345 6798 5585 7209 6830 8455 9568 3865 ... .. ..$ ATAC_snn_res.0.5 : Factor w/ 8 levels "0","1","2","3",..: 2 1 2 2 1 1 1 1 1 2 ... .. ..$ ATAC_snn_res.0.4 : Factor w/ 7 levels "0","1","2","3",..: 2 1 2 2 1 1 1 1 1 2 ... ..@ active.assay: chr "ATAC" ..@ active.ident: Factor w/ 3 levels "0","1","6": 2 1 2 2 1 1 1 1 1 2 ... .. ..- attr(, "names")= chr [1:1117] "neoTV4_AAACGAAAGCACGTAG-1" "neoTV4_AAACGAAGTTCAGTTG-1" "neoTV4_AAACGAAGTTTCACCC-1" "neoTV4_AAACTCGCAAACTACC-1" ... ..@ graphs : list() ..@ neighbors : list() ..@ reductions :List of 3 .. ..$ lsi :Formal class 'DimReduc' [package "SeuratObject"] with 9 slots .. .. .. ..@ cell.embeddings : num [1:1117, 1:50] 0.324 -0.243 0.788 0.317 0.797 ... .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. ..$ : chr [1:1117] "neoTV4_AAACGAAAGCACGTAG-1" "neoTV4_AAACGAAGTTCAGTTG-1" "neoTV4_AAACGAAGTTTCACCC-1" "neoTV4_AAACTCGCAAACTACC-1" ... .. .. .. .. .. ..$ : chr [1:50] "LSI_1" "LSI_2" "LSI_3" "LSI_4" ... .. .. .. ..@ feature.loadings : num [1:183616, 1:50] -0.00701 -0.00722 -0.0071 -0.00717 -0.0071 ... .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. ..$ : chr [1:183616] "chr17-39842748-39849073" "chr9-57070736-57078434" "chr9-124422275-124426770" "chr8-11554444-11560644" ... .. .. .. .. .. ..$ : chr [1:50] "LSI_1" "LSI_2" "LSI_3" "LSI4" ... .. .. .. ..@ feature.loadings.projected: num[0 , 0 ] .. .. .. ..@ assay.used : chr "ATAC" .. .. .. ..@ global : logi FALSE .. .. .. ..@ stdev : num [1:50] 13.21 2.16 1.82 1.59 1.32 ... .. .. .. ..@ key : chr "LSI" .. .. .. ..@ jackstraw :Formal class 'JackStrawData' [package "SeuratObject"] with 4 slots .. .. .. .. .. ..@ empirical.p.values : num[0 , 0 ] .. .. .. .. .. ..@ fake.reduction.scores : num[0 , 0 ] .. .. .. .. .. ..@ empirical.p.values.full: num[0 , 0 ] .. .. .. .. .. ..@ overall.p.values : num[0 , 0 ] .. .. .. ..@ misc :List of 5 .. .. .. .. ..$ d : num [1:50] 5659 924 780 680 567 ... .. .. .. .. ..$ u : num [1:8814, 1:50] -0.0094 -0.01553 -0.0082 -0.00599 -0.01136 ... .. .. .. .. ..$ v : num [1:183616, 1:50] -0.00701 -0.00722 -0.0071 -0.00717 -0.0071 ... .. .. .. .. ..$ iter : int 5 .. .. .. .. ..$ mprod: int 860 .. ..$ umap :Formal class 'DimReduc' [package "SeuratObject"] with 9 slots .. .. .. ..@ cell.embeddings : num [1:1117, 1:2] -4.62 1.01 -1.55 -3.47 2.2 ... .. .. .. .. ..- attr(, "dimnames")=List of 2 .. .. .. .. .. ..$ : chr [1:1117] "neoTV4_AAACGAAAGCACGTAG-1" "neoTV4_AAACGAAGTTCAGTTG-1" "neoTV4_AAACGAAGTTTCACCC-1" "neoTV4_AAACTCGCAAACTACC-1" ... .. .. .. .. .. ..$ : chr [1:2] "UMAP_1" "UMAP2" .. .. .. ..@ feature.loadings : num[0 , 0 ] .. .. .. ..@ feature.loadings.projected: num[0 , 0 ] .. .. .. ..@ assay.used : chr "ATAC" .. .. .. ..@ global : logi TRUE .. .. .. ..@ stdev : num(0) .. .. .. ..@ key : chr "UMAP" .. .. .. ..@ jackstraw :Formal class 'JackStrawData' [package "SeuratObject"] with 4 slots .. .. .. .. .. ..@ empirical.p.values : num[0 , 0 ] .. .. .. .. .. ..@ fake.reduction.scores : num[0 , 0 ] .. .. .. .. .. ..@ empirical.p.values.full: num[0 , 0 ] .. .. .. .. .. ..@ overall.p.values : num[0 , 0 ] .. .. .. ..@ misc : list() .. ..$ harmony:Formal class 'DimReduc' [package "SeuratObject"] with 9 slots .. .. .. ..@ cell.embeddings : num [1:1117, 1:50] -0.0834 -0.6384 0.4469 -0.086 0.4461 ... .. .. .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. .. .. ..$ : chr [1:1117] "neoTV4_AAACGAAAGCACGTAG-1" "neoTV4_AAACGAAGTTCAGTTG-1" "neoTV4_AAACGAAGTTTCACCC-1" "neoTV4_AAACTCGCAAACTACC-1" ... .. .. .. .. .. ..$ : chr [1:50] "harmony_1" "harmony_2" "harmony_3" "harmony4" ... .. .. .. ..@ feature.loadings : num[0 , 0 ] .. .. .. ..@ feature.loadings.projected: num[0 , 0 ] .. .. .. ..@ assay.used : chr "ATAC" .. .. .. ..@ global : logi FALSE .. .. .. ..@ stdev : num [1:50] 0.884 0.828 0.84 0.679 0.929 ... .. .. .. ..@ key : chr "harmony" .. .. .. ..@ jackstraw :Formal class 'JackStrawData' [package "SeuratObject"] with 4 slots .. .. .. .. .. ..@ empirical.p.values : num[0 , 0 ] .. .. .. .. .. ..@ fake.reduction.scores : num[0 , 0 ] .. .. .. .. .. ..@ empirical.p.values.full: num[0 , 0 ] .. .. .. .. .. ..@ overall.p.values : num[0 , 0 ] .. .. .. ..@ misc : list() ..@ images : list() ..@ project.name: chr "SeuratProject" ..@ misc : list() ..@ version :Classes 'package_version', 'numericversion' hidden list of 1 .. ..$ : int [1:3] 4 0 0 ..@ commands :List of 6 .. ..$ RunUMAP.ATAC.lsi :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots .. .. .. ..@ name : chr "RunUMAP.ATAC.lsi" .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2021-04-04 22:31:27" .. .. .. ..@ assay.used : chr "ATAC" .. .. .. ..@ call.string: chr "RunUMAP(., dims = 2:30, reduction = \"lsi\")" .. .. .. ..@ params :List of 22 .. .. .. .. ..$ dims : int [1:29] 2 3 4 5 6 7 8 9 10 11 ... .. .. .. .. ..$ reduction : chr "lsi" .. .. .. .. ..$ assay : chr "ATAC" .. .. .. .. ..$ slot : chr "data" .. .. .. .. ..$ umap.method : chr "uwot" .. .. .. .. ..$ return.model : logi FALSE .. .. .. .. ..$ n.neighbors : int 30 .. .. .. .. ..$ n.components : int 2 .. .. .. .. ..$ metric : chr "cosine" .. .. .. .. ..$ learning.rate : num 1 .. .. .. .. ..$ min.dist : num 0.3 .. .. .. .. ..$ spread : num 1 .. .. .. .. ..$ set.op.mix.ratio : num 1 .. .. .. .. ..$ local.connectivity : int 1 .. .. .. .. ..$ repulsion.strength : num 1 .. .. .. .. ..$ negative.sample.rate: int 5 .. .. .. .. ..$ uwot.sgd : logi FALSE .. .. .. .. ..$ seed.use : int 42 .. .. .. .. ..$ angular.rp.forest : logi FALSE .. .. .. .. ..$ verbose : logi TRUE .. .. .. .. ..$ reduction.name : chr "umap" .. .. .. .. ..$ reduction.key : chr "UMAP" .. ..$ NormalizeData.bodyPromoterRNA:Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots .. .. .. ..@ name : chr "NormalizeData.bodyPromoterRNA" .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2021-04-04 23:09:27" .. .. .. ..@ assay.used : chr "bodyPromoterRNA" .. .. .. ..@ call.string: chr [1:2] "NormalizeData(object = ThyVg4, assay = \"bodyPromoterRNA\", " " normalization.method = \"LogNormalize\", scale.factor = median(ThyVg4$nCount_bodyPromoterRNA))" .. .. .. ..@ params :List of 5 .. .. .. .. ..$ assay : chr "bodyPromoterRNA" .. .. .. .. ..$ normalization.method: chr "LogNormalize" .. .. .. .. ..$ scale.factor : num 15594 .. .. .. .. ..$ margin : num 1 .. .. .. .. ..$ verbose : logi TRUE .. ..$ FindNeighbors.ATAC.lsi :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots .. .. .. ..@ name : chr "FindNeighbors.ATAC.lsi" .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2021-04-04 23:11:08" .. .. .. ..@ assay.used : chr "ATAC" .. .. .. ..@ call.string: chr "FindNeighbors(object = ThyVg4, reduction = \"lsi\", dims = 2:30)" .. .. .. ..@ params :List of 17 .. .. .. .. ..$ reduction : chr "lsi" .. .. .. .. ..$ dims : int [1:29] 2 3 4 5 6 7 8 9 10 11 ... .. .. .. .. ..$ assay : chr "ATAC" .. .. .. .. ..$ k.param : num 20 .. .. .. .. ..$ return.neighbor: logi FALSE .. .. .. .. ..$ compute.SNN : logi TRUE .. .. .. .. ..$ prune.SNN : num 0.0667 .. .. .. .. ..$ nn.method : chr "annoy" .. .. .. .. ..$ n.trees : num 50 .. .. .. .. ..$ annoy.metric : chr "euclidean" .. .. .. .. ..$ nn.eps : num 0 .. .. .. .. ..$ verbose : logi TRUE .. .. .. .. ..$ force.recalc : logi FALSE .. .. .. .. ..$ do.plot : logi FALSE .. .. .. .. ..$ graph.name : chr [1:2] "ATAC_nn" "ATACsnn" .. .. .. .. ..$ l2.norm : logi FALSE .. .. .. .. ..$ cache.index : logi FALSE .. ..$ RunUMAP.ATAC.harmony :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots .. .. .. ..@ name : chr "RunUMAP.ATAC.harmony" .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2021-04-04 23:27:23" .. .. .. ..@ assay.used : chr "ATAC" .. .. .. ..@ call.string: chr "RunUMAP(ThyV4.integrated, dims = 2:30, reduction = \"harmony\")" .. .. .. ..@ params :List of 22 .. .. .. .. ..$ dims : int [1:29] 2 3 4 5 6 7 8 9 10 11 ... .. .. .. .. ..$ reduction : chr "harmony" .. .. .. .. ..$ assay : chr "ATAC" .. .. .. .. ..$ slot : chr "data" .. .. .. .. ..$ umap.method : chr "uwot" .. .. .. .. ..$ return.model : logi FALSE .. .. .. .. ..$ n.neighbors : int 30 .. .. .. .. ..$ n.components : int 2 .. .. .. .. ..$ metric : chr "cosine" .. .. .. .. ..$ learning.rate : num 1 .. .. .. .. ..$ min.dist : num 0.3 .. .. .. .. ..$ spread : num 1 .. .. .. .. ..$ set.op.mix.ratio : num 1 .. .. .. .. ..$ local.connectivity : int 1 .. .. .. .. ..$ repulsion.strength : num 1 .. .. .. .. ..$ negative.sample.rate: int 5 .. .. .. .. ..$ uwot.sgd : logi FALSE .. .. .. .. ..$ seed.use : int 42 .. .. .. .. ..$ angular.rp.forest : logi FALSE .. .. .. .. ..$ verbose : logi TRUE .. .. .. .. ..$ reduction.name : chr "umap" .. .. .. .. ..$ reduction.key : chr "UMAP" .. ..$ FindNeighbors.ATAC.harmony :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots .. .. .. ..@ name : chr "FindNeighbors.ATAC.harmony" .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2021-04-04 23:29:44" .. .. .. ..@ assay.used : chr "ATAC" .. .. .. ..@ call.string: chr [1:2] "FindNeighbors(object = ThyV4.integrated, assay = \"ATAC\", " " reduction = \"harmony\", dims = 2:30)" .. .. .. ..@ params :List of 17 .. .. .. .. ..$ reduction : chr "harmony" .. .. .. .. ..$ dims : int [1:29] 2 3 4 5 6 7 8 9 10 11 ... .. .. .. .. ..$ assay : chr "ATAC" .. .. .. .. ..$ k.param : num 20 .. .. .. .. ..$ return.neighbor: logi FALSE .. .. .. .. ..$ compute.SNN : logi TRUE .. .. .. .. ..$ prune.SNN : num 0.0667 .. .. .. .. ..$ nn.method : chr "annoy" .. .. .. .. ..$ n.trees : num 50 .. .. .. .. ..$ annoy.metric : chr "euclidean" .. .. .. .. ..$ nn.eps : num 0 .. .. .. .. ..$ verbose : logi TRUE .. .. .. .. ..$ force.recalc : logi FALSE .. .. .. .. ..$ do.plot : logi FALSE .. .. .. .. ..$ graph.name : chr [1:2] "ATAC_nn" "ATAC_snn" .. .. .. .. ..$ l2.norm : logi FALSE .. .. .. .. ..$ cache.index : logi FALSE .. ..$ FindClusters :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots .. .. .. ..@ name : chr "FindClusters" .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2021-04-04 23:29:50" .. .. .. ..@ assay.used : chr "ATAC" .. .. .. ..@ call.string: chr [1:2] "FindClusters(., algorithm = 3, resolution = 0.4, verbose = TRUE, " " graph.name = \"ATAC_snn\")" .. .. .. ..@ params :List of 10 .. .. .. .. ..$ graph.name : chr "ATAC_snn" .. .. .. .. ..$ modularity.fxn : num 1 .. .. .. .. ..$ resolution : num 0.4 .. .. .. .. ..$ method : chr "matrix" .. .. .. .. ..$ algorithm : num 3 .. .. .. .. ..$ n.start : num 10 .. .. .. .. ..$ n.iter : num 10 .. .. .. .. ..$ random.seed : num 0 .. .. .. .. ..$ group.singletons: logi TRUE .. .. .. .. ..$ verbose : logi TRUE ..@ tools : list()

timoast commented 3 years ago

Can you confirm that you tried this with Signac 1.2.0 and still see this error?

summer-tao commented 3 years ago

Signac 1.2.0

I failed to install it. Could you please help me install it? Here are the codes:

Install bioconductor

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install()

if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools") devtools::install_github("timoast/signac", ref = "develop")

Installing package into '/home/windows/Tao/R/x86_64-pc-linux-gnu-library/4.0' (as 'lib' is unspecified) ERROR: failed to lock directory ‘/home/windows/Tao/R/x86_64-pc-linux-gnu-library/4.0’ for modifying Try removing ‘/home/windows/Tao/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Signac’ Error: Failed to install 'Signac' from GitHub: (converted from warning) installation of package '/tmp/RtmpzbM1ei/file5682332af87b/Signac_1.2.0.9000.tar.gz' had non-zero exit status

And I also try: install.packages("Signac") Error in install.packages : Updating loaded packages

Restarting R session...

Error: Error occurred during transmission

timoast commented 3 years ago

Try removing ‘/home/windows/Tao/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Signac’

summer-tao commented 3 years ago

Try removing ‘/home/windows/Tao/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Signac’

Thank you, Tim. As you recommend, I delete and install the newest Signac. It works on my merged object. It is still running now. But I need to bother you again. There is an error when I run AddMotifs on the unmerged object: V4<- AddMotifs(V4, genome = BSgenome.Mmusculus.UCSC.mm10, pfm = pwm) Building motif matrix Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'matchMotifs' for signature '"PWMatrixList", "Assay"'

timoast commented 3 years ago

You should check that the active assay is a chromatin assay and not a standard assay. Closing this issue now as the original question is solved, you can open a new issue if you have any other problems