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top_markers function returning error for rowname not found #301

Closed danielgchen closed 4 years ago

danielgchen commented 4 years ago

Hi,

I was working through the tutorial for monocle and received the error below

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Error in .f(.x[[i]], ...) : object 'rowname' not found

when running

marker_test_res <- top_markers(cds, group_cells_by="partition", reference_cells=500, cores=8)

Since I only have 419 cells I thought maybe that was the issue so I dropped reference_cells down to 200 but I recieved the same error as above. Please let me know what can be done to fix this. Thanks! Below is information about my cds object:

class: cell_data_set 
dim: 1690 419 
metadata(2): cds_version citations
assays(1): counts
rownames(1690): HES4 ISG15 ... MT.CYB AC145212.1
rowData names(0):
colnames(419): AAACGGGAGGAGCGAG AAAGCAATCCAACCAA ... TTTCCTCCATCCGCGA
  TTTGTCATCTTCGGTC
colData names(2): clusters Size_Factor
reducedDimNames(3): PCA tSNE UMAP
spikeNames(0):

Below is my R session information:

R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /home/dchen/anaconda3/lib/libmkl_rt.so

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

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

other attached packages:
 [1] monocle3_0.2.0                    SingleCellExperiment_1.6.0       
 [3] umap_0.2.4.0                      lda_1.4.2                        
 [5] circlize_0.4.8                    ComplexHeatmap_2.0.0             
 [7] MultiAssayExperiment_1.10.4       BuenColors_0.5.5                 
 [9] MASS_7.3-51.3                     devtools_2.2.1                   
[11] usethis_1.5.1                     irlba_2.3.3                      
[13] plotly_4.9.1                      BSgenome.Hsapiens.UCSC.hg19_1.4.0
[15] BSgenome_1.52.0                   rtracklayer_1.44.4               
[17] Biostrings_2.52.0                 XVector_0.24.0                   
[19] SummarizedExperiment_1.14.1       DelayedArray_0.10.0              
[21] BiocParallel_1.18.1               matrixStats_0.55.0               
[23] Biobase_2.44.0                    GenomicRanges_1.36.1             
[25] GenomeInfoDb_1.20.0               IRanges_2.18.3                   
[27] S4Vectors_0.22.1                  BiocGenerics_0.30.0              
[29] motifmatchr_1.6.0                 chromVAR_1.6.0                   
[31] TFBSTools_1.22.0                  JASPAR2018_1.1.1                 
[33] forcats_0.4.0                     stringr_1.4.0                    
[35] dplyr_0.8.3                       purrr_0.3.3                      
[37] readr_1.3.1                       tidyr_1.0.0                      
[39] tibble_2.1.3                      tidyverse_1.3.0                  
[41] ggplot2_3.2.1                     SnapATAC_1.0.0                   
[43] rhdf5_2.28.1                      Matrix_1.2-17                    

loaded via a namespace (and not attached):
  [1] reticulate_1.14             R.utils_2.9.2               tidyselect_0.2.5           
  [4] poweRlaw_0.70.2             RSQLite_2.1.5               AnnotationDbi_1.46.1       
  [7] htmlwidgets_1.5.1           Rtsne_0.15                  munsell_0.5.0              
 [10] codetools_0.2-16            DT_0.11                     miniUI_0.1.1.1             
 [13] misc3d_0.8-4                withr_2.1.2                 colorspace_1.4-1           
 [16] rstudioapi_0.10             pbmcapply_1.5.0             labeling_0.3               
 [19] GenomeInfoDbData_1.2.1      farver_2.0.1                bit64_0.9-7                
 [22] rprojroot_1.3-2             Matrix.utils_0.9.7          vctrs_0.2.1                
 [25] generics_0.0.2              R6_2.4.1                    doParallel_1.0.15          
 [28] clue_0.3-57                 VGAM_1.1-2                  locfit_1.5-9.1             
 [31] bitops_1.0-6                assertthat_0.2.1            promises_1.1.0             
 [34] scales_1.1.0                gtable_0.3.0                processx_3.4.1             
 [37] seqLogo_1.50.0              rlang_0.4.2                 zeallot_0.1.0              
 [40] GlobalOptions_0.1.1         splines_3.6.0               lazyeval_0.2.2             
 [43] broom_0.5.3                 yaml_2.2.0                  reshape2_1.4.3             
 [46] modelr_0.1.5                crosstalk_1.0.0             backports_1.1.5            
 [49] httpuv_1.5.2                tools_3.6.0                 ellipsis_0.3.0             
 [52] RColorBrewer_1.1-2          sessioninfo_1.1.1           Rcpp_1.0.3                 
 [55] plyr_1.8.5                  zlibbioc_1.30.0             RCurl_1.95-4.12            
 [58] ps_1.3.0                    prettyunits_1.0.2           openssl_1.4.1              
 [61] GetoptLong_0.1.7            viridis_0.5.1               grr_0.9.5                  
 [64] ggrepel_0.8.1               haven_2.2.0                 cluster_2.0.9              
 [67] fs_1.3.1                    magrittr_1.5                RSpectra_0.16-0            
 [70] data.table_1.12.8           reprex_0.3.0                RANN_2.6.1                 
 [73] pkgload_1.0.2               hms_0.5.2                   mime_0.8                   
 [76] xtable_1.8-4                RhpcBLASctl_0.18-205        XML_3.98-1.20              
 [79] readxl_1.3.1                gridExtra_2.3               shape_1.4.4                
 [82] testthat_2.3.1              compiler_3.6.0              crayon_1.3.4               
 [85] R.oo_1.23.0                 htmltools_0.4.0             later_1.0.0                
 [88] snow_0.4-3                  RcppParallel_4.4.4          lubridate_1.7.4            
 [91] DBI_1.1.0                   dbplyr_1.4.2                rappdirs_0.3.1             
 [94] leidenbase_0.1.0            cli_2.0.0                   R.methodsS3_1.7.1          
 [97] igraph_1.2.4.2              pkgconfig_2.0.3             bigmemory.sri_0.1.3        
[100] GenomicAlignments_1.20.1    TFMPvalue_0.0.8             xml2_1.2.2                 
[103] foreach_1.4.7               annotate_1.62.0             DirichletMultinomial_1.26.0
[106] rvest_0.3.5                 callr_3.4.0                 digest_0.6.23              
[109] RcppAnnoy_0.0.14            CNEr_1.20.0                 cellranger_1.1.0           
[112] uwot_0.1.5                  edgeR_3.26.8                DelayedMatrixStats_1.6.1   
[115] shiny_1.4.0                 Rsamtools_2.0.3             gtools_3.8.1               
[118] rjson_0.2.20                lifecycle_0.1.0             nlme_3.1-140               
[121] jsonlite_1.6                Rhdf5lib_1.6.3              askpass_1.1                
[124] bigmemory_4.5.36            desc_1.2.0                  viridisLite_0.3.0          
[127] limma_3.40.6                fansi_0.4.0                 pillar_1.4.3               
[130] lattice_0.20-38             KEGGREST_1.24.1             fastmap_1.0.1              
[133] httr_1.4.1                  pkgbuild_1.0.6              GO.db_3.8.2                
[136] glue_1.3.1                  remotes_2.1.0               png_0.1-7                  
[139] iterators_1.0.12            plot3D_1.3                  bit_1.1-14                 
[142] stringi_1.4.3               blob_1.2.0                  doSNOW_1.0.18              
[145] caTools_1.17.1.3            memoise_1.1.0
danielgchen commented 4 years ago

Found that I need to set gene short name column to do this