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sulab-wmu / scPagwas

Obtain trait-relevant cell subpopulations by incorporating pathway activity transformed scRNA-seq data with GWAS data
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Error in `.rowNamesDF<-`(x, value = value) #19

Closed 1667857557 closed 9 months ago

1667857557 commented 9 months ago

您好，感谢您开发出出如此优秀的工具，我尝试在自己的工作中使用您它，但是遇到了一点小问题，在使用自己的sc-RNAs数据时报错'row.names'里不允许有遗漏值，我对我使用的数据进行了简单的检查，但没发现具体问题，请问能给我一点具体的建议吗，以下是具体报错的内容和数据结构，我使用的scpagwas包的版本是您在百度网盘上分享的

#------ Sat Nov 25 11:46:56 2023 ------## ******* 1st: Single_data_input function start! ********
** Start to filter single cell data!
Input single cell data!
6 cell types are remain, after filter!
done!
##------ Sat Nov 25 11:51:41 2023 ------## ******* 2nd: Pathway_pcascore_run function start!! ********
* Start to get Pathway SVD socre!
  |=========                                               |  17%[1] "endo"
  |===================                                     |  33%[1] "myeloids"
  |============================                            |  50%[1] "fibro"
  |=====================================                   |  67%[1] "Tcells"
  |===============================================         |  83%[1] "SMC"
  |========================================================| 100%[1] "doube"

Using score as value column: use value.var to override.
Aggregation function missing: defaulting to length
Error in `.rowNamesDF<-`(x, value = value) : 'row.names'里不允许有遗漏值
Timing stopped at: 366 35.39 414.3

然而我使用UpdateSeuratObject检查时未发现报错

> UpdateSeuratObject(sce.all)
Validating object structure
Updating object slots
Ensuring keys are in the proper structure
Ensuring feature names don't have underscores or pipes
Object representation is consistent with the most current Seurat version
An object of class Seurat 
21429 features across 64848 samples within 1 assay 
Active assay: RNA (21429 features, 2000 variable features)
 3 dimensional reductions calculated: pca, harmony, umap

以下是我使用的scRNA的结构情况

> str(sce.all)
Formal class 'Seurat' [package "SeuratObject"] with 13 slots
  ..@ assays      :List of 1
  .. ..$ RNA:Formal class 'Assay' [package "SeuratObject"] with 8 slots
  .. .. .. ..@ counts       :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. .. .. .. ..@ i       : int [1:162639385] 10 21 24 36 45 49 63 93 95 112 ...
  .. .. .. .. .. ..@ p       : int [1:64849] 0 1673 3943 6073 8123 10222 11058 13104 14505 17786 ...
  .. .. .. .. .. ..@ Dim     : int [1:2] 21429 64848
  .. .. .. .. .. ..@ Dimnames:List of 2
  .. .. .. .. .. .. ..$ : chr [1:21429] "RP11-34P13.7" "FO538757.2" "AP006222.2" "RP4-669L17.10" ...
  .. .. .. .. .. .. ..$ : chr [1:64848] "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGAGGGTGG-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATACGAT-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATGGCAC-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGGGAGTGG-1_1" ...
  .. .. .. .. .. ..@ x       : num [1:162639385] 1 1 1 1 1 1 1 14 1 2 ...
  .. .. .. .. .. ..@ factors : list()
  .. .. .. ..@ data         :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. .. .. .. .. ..@ i       : int [1:162639385] 10 21 24 36 45 49 63 93 95 112 ...
  .. .. .. .. .. ..@ p       : int [1:64849] 0 1673 3943 6073 8123 10222 11058 13104 14505 17786 ...
  .. .. .. .. .. ..@ Dim     : int [1:2] 21429 64848
  .. .. .. .. .. ..@ Dimnames:List of 2
  .. .. .. .. .. .. ..$ : chr [1:21429] "RP11-34P13.7" "FO538757.2" "AP006222.2" "RP4-669L17.10" ...
  .. .. .. .. .. .. ..$ : chr [1:64848] "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGAGGGTGG-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATACGAT-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATGGCAC-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGGGAGTGG-1_1" ...
  .. .. .. .. .. ..@ x       : num [1:162639385] 1.18 1.18 1.18 1.18 1.18 ...
  .. .. .. .. .. ..@ factors : list()
  .. .. .. ..@ scale.data   : num [1:2000, 1:64848] -0.5595 -0.5861 -0.0667 -0.8561 -0.4506 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:2000] "HES4" "ISG15" "TNFRSF18" "MXRA8" ...
  .. .. .. .. .. ..$ : chr [1:64848] "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGAGGGTGG-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATACGAT-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATGGCAC-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGGGAGTGG-1_1" ...
  .. .. .. ..@ key          : chr "rna_"
  .. .. .. ..@ assay.orig   : NULL
  .. .. .. ..@ var.features : chr [1:2000] "IL1B" "CCL4L2" "CCL3L3" "CXCL8" ...
  .. .. .. ..@ meta.features:'data.frame':  21429 obs. of  5 variables:
  .. .. .. .. ..$ vst.mean                 : num [1:21429] 0.00196 0.08424 0.1163 0.00188 0.02037 ...
  .. .. .. .. ..$ vst.variance             : num [1:21429] 0.00195 0.08739 0.12468 0.00191 0.02218 ...
  .. .. .. .. ..$ vst.variance.expected    : num [1:21429] 0.00224 0.10283 0.14261 0.00215 0.02511 ...
  .. .. .. .. ..$ vst.variance.standardized: num [1:21429] 0.874 0.85 0.874 0.89 0.883 ...
  .. .. .. .. ..$ vst.variable             : logi [1:21429] FALSE FALSE FALSE FALSE FALSE FALSE ...
  .. .. .. ..@ misc         : list()
  ..@ meta.data   :'data.frame':    64848 obs. of  17 variables:
  .. ..$ orig.ident      : chr [1:64848] "Normal_1" "Normal_1" "Normal_1" "Normal_1" ...
  .. ..$ nCount_RNA      : num [1:64848] 4407 6781 5277 5773 6518 ...
  .. ..$ nFeature_RNA    : int [1:64848] 1673 2270 2130 2050 2099 836 2046 1401 3281 2090 ...
  .. ..$ group           : chr [1:64848] "Normal" "Normal" "Normal" "Normal" ...
  .. ..$ percent_mito    : num [1:64848] 5.54 5.37 5.51 3.91 3.73 ...
  .. ..$ percent_ribo    : num [1:64848] 23.3 13.3 11.8 28 32 ...
  .. ..$ percent_hb      : num [1:64848] 0.0227 0.0147 0 0 0.046 ...
  .. ..$ RNA_snn_res.0.01: Factor w/ 4 levels "0","1","2","3": 2 3 1 2 2 4 2 2 1 2 ...
  .. ..$ seurat_clusters : Factor w/ 24 levels "0","1","2","3",..: 3 10 4 2 6 11 6 6 16 3 ...
  .. ..$ RNA_snn_res.0.05: Factor w/ 8 levels "0","1","2","3",..: 2 5 1 2 2 4 2 2 1 2 ...
  .. ..$ RNA_snn_res.0.1 : Factor w/ 9 levels "0","1","2","3",..: 2 5 1 2 2 6 2 2 1 2 ...
  .. ..$ RNA_snn_res.0.2 : Factor w/ 13 levels "0","1","2","3",..: 2 6 1 2 4 8 4 4 1 2 ...
  .. ..$ RNA_snn_res.0.3 : Factor w/ 15 levels "0","1","2","3",..: 1 8 2 1 4 10 4 4 3 1 ...
  .. ..$ RNA_snn_res.0.5 : Factor w/ 19 levels "0","1","2","3",..: 1 8 2 1 4 9 4 4 14 1 ...
  .. ..$ RNA_snn_res.0.8 : Factor w/ 24 levels "0","1","2","3",..: 2 10 5 3 6 11 6 6 16 2 ...
  .. ..$ RNA_snn_res.1   : Factor w/ 24 levels "0","1","2","3",..: 3 10 4 2 6 11 6 6 16 3 ...
  .. ..$ celltype        : chr [1:64848] "endo" "myeloids" "fibro" "endo" ...
  ..@ active.assay: chr "RNA"
  ..@ active.ident: Factor w/ 6 levels "endo","myeloids",..: 1 2 3 1 1 4 1 1 3 1 ...
  .. ..- attr(*, "names")= chr [1:64848] "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGAGGGTGG-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATACGAT-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATGGCAC-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGGGAGTGG-1_1" ...
  ..@ graphs      :List of 2
  .. ..$ RNA_nn :Formal class 'Graph' [package "SeuratObject"] with 7 slots
  .. .. .. ..@ assay.used: chr "RNA"
  .. .. .. ..@ i         : int [1:1296960] 0 2229 3735 4901 14329 14366 15767 17610 18701 22250 ...
  .. .. .. ..@ p         : int [1:64849] 0 16 24 56 87 104 123 170 180 209 ...
  .. .. .. ..@ Dim       : int [1:2] 64848 64848
  .. .. .. ..@ Dimnames  :List of 2
  .. .. .. .. ..$ : chr [1:64848] "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGAGGGTGG-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATACGAT-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATGGCAC-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGGGAGTGG-1_1" ...
  .. .. .. .. ..$ : chr [1:64848] "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGAGGGTGG-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATACGAT-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATGGCAC-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGGGAGTGG-1_1" ...
  .. .. .. ..@ x         : num [1:1296960] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. ..@ factors   : list()
  .. ..$ RNA_snn:Formal class 'Graph' [package "SeuratObject"] with 7 slots
  .. .. .. ..@ assay.used: chr "RNA"
  .. .. .. ..@ i         : int [1:4069450] 0 88 116 342 580 1747 1749 2103 2229 2289 ...
  .. .. .. ..@ p         : int [1:64849] 0 79 151 233 317 377 447 556 668 745 ...
  .. .. .. ..@ Dim       : int [1:2] 64848 64848
  .. .. .. ..@ Dimnames  :List of 2
  .. .. .. .. ..$ : chr [1:64848] "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGAGGGTGG-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATACGAT-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATGGCAC-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGGGAGTGG-1_1" ...
  .. .. .. .. ..$ : chr [1:64848] "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGAGGGTGG-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATACGAT-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATGGCAC-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGGGAGTGG-1_1" ...
  .. .. .. ..@ x         : num [1:4069450] 1 0.0811 0.0811 0.1111 0.1111 ...
  .. .. .. ..@ factors   : list()
  ..@ neighbors   : list()
  ..@ reductions  :List of 3
  .. ..$ pca    :Formal class 'DimReduc' [package "SeuratObject"] with 9 slots
  .. .. .. ..@ cell.embeddings           : num [1:64848, 1:50] 12.4 7.38 -12.86 15.75 15.37 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:64848] "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGAGGGTGG-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATACGAT-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATGGCAC-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGGGAGTGG-1_1" ...
  .. .. .. .. .. ..$ : chr [1:50] "PC_1" "PC_2" "PC_3" "PC_4" ...
  .. .. .. ..@ feature.loadings          : num [1:2000, 1:50] 0.00209 0.0018 0.00199 0.00586 -0.00885 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:2000] "IL1B" "CCL4L2" "CCL3L3" "CXCL8" ...
  .. .. .. .. .. ..$ : chr [1:50] "PC_1" "PC_2" "PC_3" "PC_4" ...
  .. .. .. ..@ feature.loadings.projected: num[0 , 0 ] 
  .. .. .. ..@ assay.used                : chr "RNA"
  .. .. .. ..@ global                    : logi FALSE
  .. .. .. ..@ stdev                     : num [1:50] 11.95 8.66 8.34 5.8 4.89 ...
  .. .. .. ..@ key                       : chr "PC_"
  .. .. .. ..@ 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 1
  .. .. .. .. ..$ total.variance: num 1549
  .. ..$ harmony:Formal class 'DimReduc' [package "SeuratObject"] with 9 slots
  .. .. .. ..@ cell.embeddings           : num [1:64848, 1:50] 12.41 6.54 -14.13 15.75 15.21 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:64848] "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGAGGGTGG-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATACGAT-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATGGCAC-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGGGAGTGG-1_1" ...
  .. .. .. .. .. ..$ : chr [1:50] "harmony_1" "harmony_2" "harmony_3" "harmony_4" ...
  .. .. .. ..@ feature.loadings          : num [1:2000, 1:50] 55895 139860 -910 -560008 103591 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:2000] "HES4" "ISG15" "TNFRSF18" "MXRA8" ...
  .. .. .. .. .. ..$ : chr [1:50] "harmony_1" "harmony_2" "harmony_3" "harmony_4" ...
  .. .. .. ..@ feature.loadings.projected: num [1:2000, 1:50] 55895 139860 -910 -560008 103591 ...
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:2000] "HES4" "ISG15" "TNFRSF18" "MXRA8" ...
  .. .. .. .. .. ..$ : chr [1:50] "harmony_1" "harmony_2" "harmony_3" "harmony_4" ...
  .. .. .. ..@ assay.used                : chr "RNA"
  .. .. .. ..@ global                    : logi FALSE
  .. .. .. ..@ stdev                     : num [1:50] 11.96 7.91 8.31 5.64 3.23 ...
  .. .. .. ..@ 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()
  .. ..$ umap   :Formal class 'DimReduc' [package "SeuratObject"] with 9 slots
  .. .. .. ..@ cell.embeddings           : num [1:64848, 1:2] 6.06 -2.87 -8.18 6.26 9.28 ...
  .. .. .. .. ..- attr(*, "scaled:center")= num [1:2] 0.2489 0.0817
  .. .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. .. ..$ : chr [1:64848] "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGAGGGTGG-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATACGAT-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGATGGCAC-1_1" "Normal_1_gene_martix.csv.gz_LZ037 AAACCCAAGGGAGTGG-1_1" ...
  .. .. .. .. .. ..$ : chr [1:2] "UMAP_1" "UMAP_2"
  .. .. .. ..@ feature.loadings          : num[0 , 0 ] 
  .. .. .. ..@ feature.loadings.projected: num[0 , 0 ] 
  .. .. .. ..@ assay.used                : chr "RNA"
  .. .. .. ..@ 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()
  ..@ images      : list()
  ..@ project.name: chr "SeuratProject"
  ..@ misc        : list()
  ..@ version     :Classes 'package_version', 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 4 1 2
  ..@ commands    :List of 8
  .. ..$ NormalizeData.RNA             :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
  .. .. .. ..@ name       : chr "NormalizeData.RNA"
  .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2023-03-03 15:21:11"
  .. .. .. ..@ assay.used : chr "RNA"
  .. .. .. ..@ call.string: chr [1:2] "NormalizeData(input_sce, normalization.method = \"LogNormalize\", " "    scale.factor = 10000)"
  .. .. .. ..@ params     :List of 5
  .. .. .. .. ..$ assay               : chr "RNA"
  .. .. .. .. ..$ normalization.method: chr "LogNormalize"
  .. .. .. .. ..$ scale.factor        : num 10000
  .. .. .. .. ..$ margin              : num 1
  .. .. .. .. ..$ verbose             : logi TRUE
  .. ..$ FindVariableFeatures.RNA      :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
  .. .. .. ..@ name       : chr "FindVariableFeatures.RNA"
  .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2023-03-03 15:21:24"
  .. .. .. ..@ assay.used : chr "RNA"
  .. .. .. ..@ call.string: chr "FindVariableFeatures(input_sce)"
  .. .. .. ..@ params     :List of 12
  .. .. .. .. ..$ assay              : chr "RNA"
  .. .. .. .. ..$ selection.method   : chr "vst"
  .. .. .. .. ..$ loess.span         : num 0.3
  .. .. .. .. ..$ clip.max           : chr "auto"
  .. .. .. .. ..$ mean.function      :function (mat, display_progress)  
  .. .. .. .. ..$ dispersion.function:function (mat, display_progress)  
  .. .. .. .. ..$ num.bin            : num 20
  .. .. .. .. ..$ binning.method     : chr "equal_width"
  .. .. .. .. ..$ nfeatures          : num 2000
  .. .. .. .. ..$ mean.cutoff        : num [1:2] 0.1 8
  .. .. .. .. ..$ dispersion.cutoff  : num [1:2] 1 Inf
  .. .. .. .. ..$ verbose            : logi TRUE
  .. ..$ ScaleData.RNA                 :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
  .. .. .. ..@ name       : chr "ScaleData.RNA"
  .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2023-03-03 15:21:28"
  .. .. .. ..@ assay.used : chr "RNA"
  .. .. .. ..@ call.string: chr "ScaleData(input_sce)"
  .. .. .. ..@ params     :List of 10
  .. .. .. .. ..$ features          : chr [1:2000] "IL1B" "CCL4L2" "CCL3L3" "CXCL8" ...
  .. .. .. .. ..$ assay             : chr "RNA"
  .. .. .. .. ..$ model.use         : chr "linear"
  .. .. .. .. ..$ use.umi           : logi FALSE
  .. .. .. .. ..$ do.scale          : logi TRUE
  .. .. .. .. ..$ do.center         : logi TRUE
  .. .. .. .. ..$ scale.max         : num 10
  .. .. .. .. ..$ block.size        : num 1000
  .. .. .. .. ..$ min.cells.to.block: num 3000
  .. .. .. .. ..$ verbose           : logi TRUE
  .. ..$ RunPCA.RNA                    :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
  .. .. .. ..@ name       : chr "RunPCA.RNA"
  .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2023-03-03 15:21:58"
  .. .. .. ..@ assay.used : chr "RNA"
  .. .. .. ..@ call.string: chr "RunPCA(input_sce, features = VariableFeatures(object = input_sce))"
  .. .. .. ..@ params     :List of 11
  .. .. .. .. ..$ assay          : chr "RNA"
  .. .. .. .. ..$ features       : chr [1:2000] "IL1B" "CCL4L2" "CCL3L3" "CXCL8" ...
  .. .. .. .. ..$ npcs           : num 50
  .. .. .. .. ..$ rev.pca        : logi FALSE
  .. .. .. .. ..$ weight.by.var  : logi TRUE
  .. .. .. .. ..$ verbose        : logi TRUE
  .. .. .. .. ..$ ndims.print    : int [1:5] 1 2 3 4 5
  .. .. .. .. ..$ nfeatures.print: num 30
  .. .. .. .. ..$ reduction.name : chr "pca"
  .. .. .. .. ..$ reduction.key  : chr "PC_"
  .. .. .. .. ..$ seed.use       : num 42
  .. ..$ Seurat..ProjectDim.RNA.harmony:Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
  .. .. .. ..@ name       : chr "Seurat::ProjectDim.RNA.harmony"
  .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2023-03-03 15:22:43"
  .. .. .. ..@ assay.used : chr "RNA"
  .. .. .. ..@ call.string: chr [1:2] "Seurat::ProjectDim(object, reduction = reduction.save, overwrite = TRUE, " "    verbose = FALSE)"
  .. .. .. ..@ params     :List of 7
  .. .. .. .. ..$ reduction      : chr "harmony"
  .. .. .. .. ..$ assay          : chr "RNA"
  .. .. .. .. ..$ dims.print     : int [1:5] 1 2 3 4 5
  .. .. .. .. ..$ nfeatures.print: num 20
  .. .. .. .. ..$ overwrite      : logi TRUE
  .. .. .. .. ..$ do.center      : logi FALSE
  .. .. .. .. ..$ verbose        : logi FALSE
  .. ..$ RunUMAP.RNA.harmony           :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
  .. .. .. ..@ name       : chr "RunUMAP.RNA.harmony"
  .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2023-03-03 15:24:00"
  .. .. .. ..@ assay.used : chr "RNA"
  .. .. .. ..@ call.string: chr "RunUMAP(seuratObj, dims = 1:15, reduction = \"harmony\")"
  .. .. .. ..@ params     :List of 26
  .. .. .. .. ..$ dims                : int [1:15] 1 2 3 4 5 6 7 8 9 10 ...
  .. .. .. .. ..$ reduction           : chr "harmony"
  .. .. .. .. ..$ assay               : chr "RNA"
  .. .. .. .. ..$ 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
  .. .. .. .. ..$ densmap             : logi FALSE
  .. .. .. .. ..$ dens.lambda         : num 2
  .. .. .. .. ..$ dens.frac           : num 0.3
  .. .. .. .. ..$ dens.var.shift      : num 0.1
  .. .. .. .. ..$ verbose             : logi TRUE
  .. .. .. .. ..$ reduction.name      : chr "umap"
  .. .. .. .. ..$ reduction.key       : chr "UMAP_"
  .. ..$ FindNeighbors.RNA.harmony     :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
  .. .. .. ..@ name       : chr "FindNeighbors.RNA.harmony"
  .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2023-03-03 15:24:14"
  .. .. .. ..@ assay.used : chr "RNA"
  .. .. .. ..@ call.string: chr "FindNeighbors(input_sce, reduction = \"harmony\", dims = 1:15)"
  .. .. .. ..@ params     :List of 17
  .. .. .. .. ..$ reduction      : chr "harmony"
  .. .. .. .. ..$ dims           : int [1:15] 1 2 3 4 5 6 7 8 9 10 ...
  .. .. .. .. ..$ assay          : chr "RNA"
  .. .. .. .. ..$ 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] "RNA_nn" "RNA_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: "2023-03-03 15:27:21"
  .. .. .. ..@ assay.used : chr "RNA"
  .. .. .. ..@ call.string: chr "FindClusters(input_sce.all, resolution = res, algorithm = 1)"
  .. .. .. ..@ params     :List of 10
  .. .. .. .. ..$ graph.name      : chr "RNA_snn"
  .. .. .. .. ..$ modularity.fxn  : num 1
  .. .. .. .. ..$ resolution      : num 1
  .. .. .. .. ..$ method          : chr "matrix"
  .. .. .. .. ..$ algorithm       : num 1
  .. .. .. .. ..$ n.start         : num 10
  .. .. .. .. ..$ n.iter          : num 10
  .. .. .. .. ..$ random.seed     : num 0
  .. .. .. .. ..$ group.singletons: logi TRUE
  .. .. .. .. ..$ verbose         : logi TRUE
  ..@ tools       : list()
dengchunyu commented 9 months ago

可能是因为你更新了所有安装包，导致了错误，之前有一个人和你遇到了同样的问题，他的操作就是每一次安装包都要更新所有依赖包。解决方法：先删除RMTstat，bigreadr，Matrix，irlba以及scPagwas,并且重新安装scPagwas，安装过程中提醒更新时空格直接跳过，不要随便更新之前安装的包，万一不兼容就会出问题。对于依赖包更新后可能报错的问题将在之后解决

1667857557 commented 9 months ago

可能是因为你更新了所有安装包，导致了错误，之前有一个人和你遇到了同样的问题，他的操作就是每一次安装包都要更新所有依赖包。解决方法：先删除RMTstat，bigreadr，Matrix，irlba以及scPagwas,并且重新安装scPagwas，安装过程中提醒更新时空格直接跳过，不要随便更新之前安装的包，万一不兼容就会出问题。对于依赖包更新后可能报错的问题将在之后解决

感谢您的及时回复，按照您的操作后确实可以正常运行了，祝您工作顺利