star_to_mat: Convert STAR read counts to count matrix.

In vari-bbc/bbcRNA: Bulk RNA-seq workflow for VAI BBC

Description

star_to_mat returns a count matrix from STAR ReadsPerGene.out.tab files.

Usage

star_to_mat(dir, rgx, column, rm_ens_vers = TRUE)

Arguments

dir	A character scalar indicating the directory containing all the STAR ReadsPerGene.out.tab files.
rgx	A character scalar representing a regex used to parse out the sample name from the name of the ReadsPerGene.out.tab file.
column	An integer indicating the column to extract counts from. 1 = unstranded, 2 = 1st read strand aligned with RNA, 3 = 2nd read strand aligned with RNA with RNA
rm_ens_vers	Logical indicating whether version number should be removed from gene ID (as indicated by trailing period and integers).

Details

This function will read in all the '*ReadsPerGene.out.tab' files in the specified directory and converts it to a counts matrix.

Value

A matrix where the column names are the sample names and the row names are the gene names

vari-bbc/bbcRNA documentation built on Nov. 10, 2020, 11:09 p.m.