build_gaf: Build gene annotation

In hyochoi/SCISSOR: Shape changes in selecting sample outliers in RNA-seq

Build gene annotation

Description

Get gene annotation ranges (exons) for all genes from a GTF file.

Usage

build_gaf(GTF.file = NULL, output.file = NULL)

Arguments

GTF.file	GTF file name (with full directory). If NULL, UCSC annotation databases will be used.
output.file	an output file name where the gene annotation ranges will be saved

Examples

GTF.file = "genes.gtf"
regions = build_gaf(GTF.file=GTF.file)
write.table(x=regions,file="genes_gaf.txt",sep="\t",quote=F,row.names=F)

hyochoi/SCISSOR documentation built on July 6, 2022, 6:59 a.m.