RNAseqDegs_DESeq: Helper Function For DEG Analysis of RNA-seq Data using DESeq

In lusystemsbio/NetAct: NetAct -- a computational platform to construct core transcription factor regulatory networks using gene activity

Helper Function For DEG Analysis of RNA-seq Data using DESeq

Description

Helper Function For DEG Analysis of RNA-seq Data using DESeq

Usage

RNAseqDegs_DESeq(counts, phenodata, complist, qval = 0.05)

Arguments

counts	Processed gene expression count data
phenodata	pData that provides batch & experimental conditions
complist	a vector of multiple comparisons in the format of contrasts in limma (e.g. c("A-B", "A-C", "B-C"))
qval	q-value cutoff for DEG analysis (default: 0.05)

Value

DEresult: a list of DEG results, including those for each single comparison and those for the overall comparison. Each DEG result is in the format of A list containing: table: table of DEG results. rank_vector: a vector of t-statistics for every gene. degs: a vector of gene symbols for DEGs. e: expression data (CPM).

lusystemsbio/NetAct documentation built on Sept. 7, 2024, 8:34 p.m.