movDEGene: Get DE genes

In BMILAB/movAPA: movAPA: Modeling and Visualization of Dynamics of Alternative PolyAdenylation

Get DE genes

Description

movDEGene first summerizes all PACs in a gene to get gene expression level, and then calls DESeq2 for DE analysis. It performs DE analyses for all condition pairs of the given group. If you only need a specific condition pair, call subsetPACds() first to filter used conditions.

Usage

movDEGene(PACds, group, method = "DESeq2", minSumPAT = 10)

Arguments

PACds	a PACdataset.
group	a sample group name to get all conditions under the group.
method	only DESeq2 is allowed for now
minSumPAT	filter genes with total PAT number across all conditions >=minSumPAT

Value

An object of movDEGeneRes, with slots[group, conds, pairwise=list[value=log2FC_<cond1.cond2>, padj=padj_<cond1.cond2>]]

See Also

Other comparison functions: movAPAindexDiff(), movAPAindex(), movAPAswitch(), movDEPAC(), movPAindex(), movUTRtrend(), plotCummPAindex()

Examples

data(PACds)
## Detect DE genes for two conditions.
## Subset two conditions first.
pacds=subsetPACds(PACds, group='group',cond1='anther', cond2='embryo')
## Detect DE genes using DESeq2 method,
## only genes with total read counts in all samples >=50 are used.
DEgene=movDEGene(PACds=pacds, method='DESeq2', group='group', minSumPAT=50)
## Detect DE genes in all pairwise conditions.
DEgene=movDEGene(PACds=PACds, method='DESeq2', group='group', minSumPAT=50)

BMILAB/movAPA documentation built on Jan. 3, 2024, 11:09 p.m.