SingleCellExperiment。为什么在单单元格实验中无法成功更改行名和列名？

Question

我必须处理一些数据才能深入了解腺癌。为了获得更多见解，我必须操纵我的数据。到目前为止，我的管道如下：

nsclc <- read.table("D:\\Bioinformatica\\Project Work and PhD Proposal\\Data\\Data Extracted\\GSE143423_lbm_scRNAseq_gene_expression_counts.csv",
header=TRUE,sep=",")

meta_1 <- read.table("D:\\Bioinformatica\\Project Work and PhD Proposal\\Data\\Data Extracted\\GSE143423_lbm_scRNAseq_metadata.csv",
header = TRUE,sep =",")

meta_1$X <- NULL
#......Creation of first Single cell Experiment

sce_lc <- SingleCellExperiment(
assays = list(counts = as.matrix(nsclc)),
rowData =nsclc[1:dim(nsclc)[1],1] %>% data.frame ,
colData = cell <- paste0("cell_",1:dim(nsclc)[2]) %>% data.frame,metadata = meta_1)                                                                                      

当我探索sce_lc实验时，行名没有变化，而行名也没有变化。谁能帮我吗？

Answer 1

您需要命名矩阵的行。在开始旅程之前，请先阅读vignette。 rowData和colData是其他东西。您只需在插入矩阵之前指定矩阵的行名和列名即可。在创建对象时避免使用管道。.有些分配确实很奇怪：

library(SingleCellExperiment)

nsclc = data.frame(what=paste0("gene",1:100),
matrix(rnbinom(1000,mu=100,size=1),ncol=10,nrow=10))
meta_1 = data.frame(id=1:10,var=letters[1:10])

rownames(nsclc) = as.character(nsclc[,1])
colnames(nsclc) = paste0("cell_",1:ncol(nsclc))

sce_lc <- SingleCellExperiment(
assays = list(counts = as.matrix(nsclc[,-1])),
metadata = meta_1)

class: SingleCellExperiment 
dim: 100 10 
metadata(2): id var
assays(1): counts
rownames(100): gene1 gene2 ... gene99 gene100
rowData names(0):
colnames(10): cell_2 cell_3 ... cell_10 cell_11
colData names(0):
reducedDimNames(0):
spikeNames(0):