Question

我有一个看起来像这样的R代码：

r <- rowData(sce_list[[1]])
c <- colData(sce_list[[1]])
t <- sce_list[[1]][r$use,c$use]

到这里一切运行顺利。但是，当我尝试将t的值分配给另一个对象，如下所示时，我会遇到错误。

sce_list[[1]]$qc = t

Error in `[[<-`(`*tmp*`, name, value = <S4 object of class "SingleCellExperiment">) : 
  1842 elements in value to replace 5586 elements

其中sce_list是sce的列表。

编辑：

str（t）的输出

Formal class 'SingleCellExperiment' [package "SingleCellExperiment"] with 10 slots
  ..@ int_elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
  .. .. ..@ rownames       : NULL
  .. .. ..@ nrows          : int 1842
  .. .. ..@ listData       :List of 2
  .. .. .. ..$ is_spike_MT: logi [1:1842] FALSE FALSE FALSE FALSE FALSE FALSE ...
  .. .. .. ..$ is_spike   : logi [1:1842] FALSE FALSE FALSE FALSE FALSE FALSE ...
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ int_colData        :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
  .. .. ..@ rownames       : NULL
  .. .. ..@ nrows          : int 3973
  .. .. ..@ listData       : Named list()
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ int_metadata       :List of 2
  .. ..$ version    :Classes 'package_version', 'numeric_version'  hidden list of 1
  .. .. ..$ : int [1:3] 1 0 0
  .. ..$ spike_names: chr "MT"
  ..@ reducedDims        :Formal class 'SimpleList' [package "S4Vectors"] with 4 slots
  .. .. ..@ listData       : Named list()
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ rowRanges          :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots
  .. .. ..@ unlistData     :Formal class 'GRanges' [package "GenomicRanges"] with 6 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 "integer"
  .. .. .. .. .. .. ..@ 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()
  .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
  .. .. .. .. .. .. ..@ rownames       : NULL
  .. .. .. .. .. .. ..@ nrows          : int 0
  .. .. .. .. .. .. ..@ listData       : Named list()
  .. .. .. .. .. .. ..@ elementType    : chr "ANY"
  .. .. .. .. .. .. ..@ 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) 
  .. .. .. .. ..@ metadata       : list()
  .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
  .. .. .. .. ..@ rownames       : NULL
  .. .. .. .. ..@ nrows          : int 1842
  .. .. .. .. ..@ listData       :List of 12
  .. .. .. .. .. ..$ id                   : chr [1:1842] "ENSG00000187608" "ENSG00000186891" "ENSG00000186827" "ENSG00000175756" ...
  .. .. .. .. .. ..$ symbol               : chr [1:1842] "ISG15" "TNFRSF18" "TNFRSF4" "AURKAIP1" ...
  .. .. .. .. .. ..$ is_feature_control   : logi [1:1842] FALSE FALSE FALSE FALSE FALSE FALSE ...
  .. .. .. .. .. ..$ is_feature_control_MT: logi [1:1842] FALSE FALSE FALSE FALSE FALSE FALSE ...
  .. .. .. .. .. ..$ mean_counts          : num [1:1842] 5.067 0.166 0.162 0.639 0.719 ...
  .. .. .. .. .. ..$ log10_mean_counts    : num [1:1842] 0.783 0.0669 0.0651 0.2146 0.2353 ...
  .. .. .. .. .. ..$ rank_counts          : num [1:1842] 33536 30766 30710 32857 32945 ...
  .. .. .. .. .. ..$ n_cells_counts       : int [1:1842] 4580 516 458 2376 2578 2153 2277 5388 3604 4131 ...
  .. .. .. .. .. ..$ pct_dropout_counts   : num [1:1842] 18 90.8 91.8 57.5 53.8 ...
  .. .. .. .. .. ..$ total_counts         : num [1:1842] 28305 930 904 3569 4017 ...
  .. .. .. .. .. ..$ log10_total_counts   : num [1:1842] 4.45 2.97 2.96 3.55 3.6 ...
  .. .. .. .. .. ..$ use                  : Named logi [1:1842] TRUE TRUE TRUE TRUE TRUE TRUE ...
  .. .. .. .. .. .. ..- attr(*, "names")= chr [1:1842] "ENSG00000187608" "ENSG00000186891" "ENSG00000186827" "ENSG00000175756" ...
  .. .. .. .. ..@ elementType    : chr "ANY"
  .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. ..@ metadata       : list()
  .. .. ..@ partitioning   :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots
  .. .. .. .. ..@ end            : int [1:1842] 0 0 0 0 0 0 0 0 0 0 ...
  .. .. .. .. ..@ NAMES          : chr [1:1842] "ENSG00000187608" "ENSG00000186891" "ENSG00000186827" "ENSG00000175756" ...
  .. .. .. .. ..@ elementType    : chr "integer"
  .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. ..@ metadata       : list()
  .. .. ..@ elementType    : chr "GRanges"
  .. .. ..@ metadata       : list()
  ..@ colData            :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
  .. .. ..@ rownames       : chr [1:3973] "AAACCTGAGAAGGTTT-1" "AAACCTGAGCGTTCCG-1" "AAACCTGAGTACGTAA-1" "AAACCTGGTCCATGAT-1" ...
  .. .. ..@ nrows          : int 3973
  .. .. ..@ listData       :List of 32
  .. .. .. ..$ dataset                               : int [1:3973] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. ..$ barcode                               : chr [1:3973] "AAACCTGAGAAGGTTT-1" "AAACCTGAGCGTTCCG-1" "AAACCTGAGTACGTAA-1" "AAACCTGGTCCATGAT-1" ...
  .. .. .. ..$ total_features                        : int [1:3973] 1373 1837 2259 2601 1967 1236 1642 1153 1078 2682 ...
  .. .. .. ..$ log10_total_features                  : num [1:3973] 3.14 3.26 3.35 3.42 3.29 ...
  .. .. .. ..$ total_counts                          : num [1:3973] 3380 7332 10099 12184 7352 ...
  .. .. .. ..$ log10_total_counts                    : num [1:3973] 3.53 3.87 4 4.09 3.87 ...
  .. .. .. ..$ pct_counts_top_50_features            : num [1:3973] 33.1 38.9 42.5 42.2 42.8 ...
  .. .. .. ..$ pct_counts_top_100_features           : num [1:3973] 45 54.8 59.2 53.5 52.4 ...
  .. .. .. ..$ pct_counts_top_200_features           : num [1:3973] 57.5 66.9 69 64.7 63.5 ...
  .. .. .. ..$ pct_counts_top_500_features           : num [1:3973] 74.2 79.2 79.4 76.8 76.6 ...
  .. .. .. ..$ total_features_endogenous             : int [1:3973] 1373 1837 2259 2601 1967 1236 1642 1153 1078 2682 ...
  .. .. .. ..$ log10_total_features_endogenous       : num [1:3973] 3.14 3.26 3.35 3.42 3.29 ...
  .. .. .. ..$ total_counts_endogenous               : num [1:3973] 3380 7332 10099 12184 7352 ...
  .. .. .. ..$ log10_total_counts_endogenous         : num [1:3973] 3.53 3.87 4 4.09 3.87 ...
  .. .. .. ..$ pct_counts_endogenous                 : num [1:3973] 100 100 100 100 100 100 100 100 100 100 ...
  .. .. .. ..$ pct_counts_top_50_features_endogenous : num [1:3973] 33.1 38.9 42.5 42.2 42.8 ...
  .. .. .. ..$ pct_counts_top_100_features_endogenous: num [1:3973] 45 54.8 59.2 53.5 52.4 ...
  .. .. .. ..$ pct_counts_top_200_features_endogenous: num [1:3973] 57.5 66.9 69 64.7 63.5 ...
  .. .. .. ..$ pct_counts_top_500_features_endogenous: num [1:3973] 74.2 79.2 79.4 76.8 76.6 ...
  .. .. .. ..$ total_features_feature_control        : int [1:3973] 0 0 0 0 0 0 0 0 0 0 ...
  .. .. .. ..$ log10_total_features_feature_control  : num [1:3973] 0 0 0 0 0 0 0 0 0 0 ...
  .. .. .. ..$ total_counts_feature_control          : num [1:3973] 0 0 0 0 0 0 0 0 0 0 ...
  .. .. .. ..$ log10_total_counts_feature_control    : num [1:3973] 0 0 0 0 0 0 0 0 0 0 ...
  .. .. .. ..$ pct_counts_feature_control            : num [1:3973] 0 0 0 0 0 0 0 0 0 0 ...
  .. .. .. ..$ total_features_MT                     : int [1:3973] 0 0 0 0 0 0 0 0 0 0 ...
  .. .. .. ..$ log10_total_features_MT               : num [1:3973] 0 0 0 0 0 0 0 0 0 0 ...
  .. .. .. ..$ total_counts_MT                       : num [1:3973] 0 0 0 0 0 0 0 0 0 0 ...
  .. .. .. ..$ log10_total_counts_MT                 : num [1:3973] 0 0 0 0 0 0 0 0 0 0 ...
  .. .. .. ..$ pct_counts_MT                         : num [1:3973] 0 0 0 0 0 0 0 0 0 0 ...
  .. .. .. ..$ is_cell_control                       : logi [1:3973] FALSE FALSE FALSE FALSE FALSE FALSE ...
  .. .. .. ..$ use                                   : logi [1:3973] TRUE TRUE TRUE TRUE TRUE TRUE ...
  .. .. .. ..$ outlier                               : logi [1:3973] FALSE FALSE FALSE FALSE FALSE FALSE ...
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ assays             :Reference class 'ShallowSimpleListAssays' [package "SummarizedExperiment"] with 1 field
  .. ..$ data: NULL
  .. ..and 14 methods.
  ..@ NAMES              : NULL
  ..@ elementMetadata    :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
  .. .. ..@ rownames       : NULL
  .. .. ..@ nrows          : int 1842
  .. .. ..@ listData       : Named list()
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ metadata           :List of 1
  .. ..$ name: chr "iMates-1"

和

class(sce_list[[1]])
[1] "SingleCellExperiment"
attr(,"package")
[1] "SingleCellExperiment"

R大师的任何人都可以帮助我解决这个问题。

Answer 1

我想出了一种解决此问题的方法。这不是最优雅的答案，但确实可以解决问题。因此，这里是：

for (i in seq_along(sce_list))
 {
     r <- rowData(sce_list[[i]])$use
     c <- colData(sce_list[[i]])$use
     tt=(sce_list[[i]])[r,c]
      assign(paste0("sce_",i,".qc"),tt)
 }

是的，我把它放在一个循环中，因为我希望它可以循环运行。：）

如果某人有这样做的优雅方法，请发布它，我会尝试的。

将值分配给列表列表时出错

1 个答案: