How to split grouping information in a single expression matrix?
1
Hello everyone,
I am a rookie in single-cell RNA seq analysis. Currently, I am learning to analyze the data (GSE150703) in R. The colname is like NORM_P14_WR_Mccarrol_r3_CGGTAATTGCCC
and OIR_P17_WR_Joyal_r1_TCGCGCCACTAG
. When I read the table and created a Seuratobject I found the orig.ident
only contains NORM
. How can I split the grouping information into four groups such as NORM P14
, NORM P17
, OIR P14
, OIR P17
?
Thank you tons.
scRNA-seq
GEO
Seurat
• 595 views
Please do this to create Seurat object from GSE150703 data-
library(data.table)
ftp="https://ftp.ncbi.nlm.nih.gov/geo/series/GSE150nnn/GSE150703/suppl/GSE150703_retina_NORM_OIR_P14_P17_C57_WR_CD73FT_noamg_normalizedUMI_Count_DGEmatrix.txt.gz"
counts <-data.table::fread(ftp)
rownames(counts)=counts$V1
counts[1:5,1:5]
V1 NORM_P14_WR_Mccarrol_r3_CGGTAATTGCCC NORM_P14_WR_Mccarrol_r5_AGTACCGTAAGG NORM_P14_WR_Mccarrol_r5_CTAATAAAGCTC NORM_P14_WR_Mccarrol_r2_CGCCGATAGATG
1: 0610005C13RIK 0 0 0 0.000000
2: 0610007N19RIK 0 0 0 0.000000
3: 0610007P14RIK 0 0 0 3.267762
4: 0610009B14RIK 0 0 0 0.000000
5: 0610009B22RIK 0 0 0 0.000000
counts$V1 <- NULL
seurat_obj=CreateSeuratObject(counts)
seurat_obj
An object of class Seurat
21408 features across 31271 samples within 1 assay
Active assay: RNA (21408 features, 0 variable features)
1 layer present: counts
head(seurat_obj@meta.data)
orig.ident nCount_RNA nFeature_RNA
NORM_P14_WR_Mccarrol_r3_CGGTAATTGCCC NORM 1040.047 301
NORM_P14_WR_Mccarrol_r5_AGTACCGTAAGG NORM 1002.495 296
NORM_P14_WR_Mccarrol_r5_CTAATAAAGCTC NORM 1079.672 326
NORM_P14_WR_Mccarrol_r2_CGCCGATAGATG NORM 1023.541 299
NORM_P14_WR_Mccarrol_r6_TAGAGTCGAGCC NORM 1117.872 362
NORM_P14_WR_Mccarrol_r3_CCGACTCCCCAA NORM 1579.136 567
#changing orig.ident in the following steps
seurat_obj@meta.data$Idents=rownames(seurat_obj@meta.data)
seurat_obj@meta.data$Idents=stringr::str_extract(seurat_obj@meta.data$Idents, "[^_]*_[^_]*")
seurat_obj@meta.data$orig.ident <- NULL
seurat_obj@meta.data$orig.ident <- seurat_obj@meta.data$Idents
seurat_obj@meta.data$Idents <- NULL
head(seurat_obj@meta.data)
nCount_RNA nFeature_RNA orig.ident
NORM_P14_WR_Mccarrol_r3_CGGTAATTGCCC 1040.047 301 NORM_P14
NORM_P14_WR_Mccarrol_r5_AGTACCGTAAGG 1002.495 296 NORM_P14
NORM_P14_WR_Mccarrol_r5_CTAATAAAGCTC 1079.672 326 NORM_P14
NORM_P14_WR_Mccarrol_r2_CGCCGATAGATG 1023.541 299 NORM_P14
NORM_P14_WR_Mccarrol_r6_TAGAGTCGAGCC 1117.872 362 NORM_P14
NORM_P14_WR_Mccarrol_r3_CCGACTCCCCAA 1579.136 567 NORM_P14
table(seurat_obj@meta.data$orig.ident)
NORM_P14 NORM_P17 OIR_P14 OIR_P17
10332 3450 9590 7899
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15 months ago by
bk11
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