movDEPAC: Get DE PACs

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

Get DE PACs

Description

movDEPAC calls DESeq2/DEXSeq or uses chisq.test 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

movDEPAC(PACds, group, method = "DESeq2", minSumPAT = 10, chisqPadjust = TRUE)

Arguments

PACds	a PACdataset.
group	a sample group name to get all conditions under the group.
method	can be DEXseq, DESeq2, chisq, ignoring cases. chisq is as in Shulman 2019 et al, which first performs chisq.test for all PACs in a gene to filter sig. genes and then performs chisq.test for each PAC. If there are multiple reps, then will pool reps first before chisq.
minSumPAT	filter PACs with total PAT number across all conditions >=minSumPAT
chisqPadjust	if T then output adjust pvalues instead of raw pvalues.

Value

An object of movDEPACRes, including slots [group, conds, pairwise=list[value=log2FC_<cond1.cond2> for DESeq2/DEXSeq; 1-genePv for Chisq, padj=padj_<cond1.cond2>], PACusage(if method=DEXseq)]

See Also

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

Examples

data(PACds)
## Detect DE PACs in all pairwise conditions using DESeq2 method,
## only PACs with total read counts in all samples >=20 are used.
DEPAC=movDEPAC(PACds, method='DESeq2', group='group', minSumPAT=20)

## Detect DE PACs using DEXseq method (may be slow).
DEXPAC=movDEPAC(PACds, method='DEXseq', group='group', minSumPAT=20)

## Detect DE PACs using chisq-PACdsPAS method.
DEqPAC=movDEPAC(PACds, method='chisq', group='group', minSumPAT=20)

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