How to use gsub inside mapply to assign names to Seurat objects
I wanted to assign the name of the matrix file after substituting the suffix to the corresponding Seurat object that is created.
I wrote the function for multiple files as below:
read_atac <- function(sc_matrix, sc_frag, sc_meta){
name <-gsub('filtered_peak_bc_matrix.h5','',sc_matrix)
counts <- Read10X_h5(filename = sc_matrix)
chrom_assay <- CreateChromatinAssay(
counts = counts,
sep = c(":", "-"),
genome = 'hg38',
fragments = sc_frag,
min.cells = 10,
min.features = 200
)
meta <- read.csv(
file = sc_meta,
header = TRUE,
row.names = 1)
assign(name, CreateSeuratObject(counts = chrom_assay, assay = "peaks", meta.data = meta))
}
mapply(read_atac, sc_matrix, sc_frag, sc_meta).
But, Seurat objects are created with the full name of the matrix file. gsub is not working.
$`GSM8002547_Chr-Veh_R1_filtered_peak_bc_matrix.h5`
An object of class Seurat
268284 features across 4316 samples within 1 assay
Active assay: peaks (268284 features, 0 variable features)
2 layers present: counts, data
I want object names as only 'GSM8002547_Chr-Veh_R1', 'GSM8002548_Chr-Veh_R2' and so on
sc_matrix has a list of matrix files
sc_matrix
[1] "GSM8002547_Chr-Veh_R1_filtered_peak_bc_matrix.h5"
[2] "GSM8002548_Chr-Veh_R2_filtered_peak_bc_matrix.h5"
[3] "GSM8002549_Veh-Veh_R1_filtered_peak_bc_matrix.h5"
[4] "GSM8002550_Veh-Veh_R2_filtered_peak_bc_matrix.h5"
I tried printing the name inside the function, it prints the name correctly but doesn't assign the name to seurat object
1 answer
I found the answer
I stored the output of mapply to a variable. Then I used for loop to assign() names to individual objects
# assign names to seurat object list obtained from previous step
for (i in 1:length(sc_matrix)){
name <-gsub('_filtered_peak_bc_matrix.h5','_seurat',sc_matrix[i])
assign(name, seurat_list[i])
}
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