getSign: getSign genes as table with test data

In perllb/deseqAbstraction: A set of functions to make DESeq pipes more smooth

getSign genes as table with test data

Description

Get the significantly changed genes, returning deseq-table with up and down-regulated genes separately in a list.

Usage

getSign(x, p = 0.01, l = 0.2)

Arguments

x:	object of results(dds), or a data.frame with column named "padj" with adjusted p-values, and one named "log2FoldChange" with log2(fold changes)
p:	p-adj cutoff to use
l:	log2(fc) cutoff to use

Examples

test <- results(dds,contrast = c("condition","genex-KO","WT"))
sign <- getSign(x = test, p = 0.01, l = 0.5)
up <- sign$up
down <- sign$down

perllb/deseqAbstraction documentation built on Oct. 31, 2023, 2:13 a.m.