This function imports a DESeq2 object from nfcore ATAC-seq pipeline output and adds gene names.
Usage
import_nfcore_atac(rdata, annotatePeaks, dist.to.TSS = 2000)
Arguments
- rdata
Path to the RData file containing the DESeq2 object
- dist.to.TSS
Distance to TSS to consider as TSS. Default is 2000
- tx2gene
Path to the tx2gene mapping file
Value
A DESeq2 object with gene names added to rowData
Examples
if (FALSE) { # \dontrun{
# Import DESeq2 object and add gene names
dds <- import_nfcore_atac("path/to/dds.RData", "path/to/tx2gene.tsv")
} # }