selectGenes: Function to select genes from time course Abx RNAseq data

In nirmalya-broad/GeneSelection: Generate selection method for diagnostics project

Description

This is the main function to generate genes from Abx RNAseq time course data

Usage

selectGenes(count_file, outdir, stag, l_cand = 1, base_lim = 50,
  use_t1 = FALSE, use_res = FALSE)

Arguments

count_file	File containing read counts for genes for all samples
outdir	Output directory for results and logs
stag	A string appeded to the generated files
l_cand	log2fold change limit for candidate genes [default : 1]
base_lim	baseMean limits for a gene after DESeq2 [default: 50]
use_t1	Set it to use first time point [default: FALSE]
use_res	Set to use resistant strains [default: FALSE]

Examples

selectGenes()

nirmalya-broad/GeneSelection documentation built on April 19, 2020, 6:12 p.m.