movUTRtrend: Analyze 3' UTR shortening/lengthening.

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

Analyze 3' UTR shortening/lengthening.

Description

movUTRtrend uses three methods for analysis of 3' UTR shortening/lengthening (or called 3' UTR switching). It performs 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

movUTRtrend(
  PACds,
  group,
  method = "linearTrend",
  avgPACtag = 5,
  avgGeneTag = 10,
  aMovDEPACRes = NULL,
  DEPAC.padjThd = 0.1,
  mindist = 50,
  fisherThd = 0.1,
  logFCThd = 1,
  selectOne = "farest"
)

Arguments

PACds	a PACdataset.
group	a sample group name to get all conditions under the group.
method	can be linearTrend, DE, DEX.
avgPACtag	filter PACs with average tag number between cond1-cond2 >= avgPACtag.
avgGeneTag	the same as avgPACtag but for gene.
aMovDEPACRes	used only for method=DE/DEX, an object of movDEPACRes to get DE PAC results.
DEPAC.padjThd	used only for method=DE/DEX, to filter DE PACs with padj<DEPAC.padjThd.
mindist	mindist and fisherThd,logFCThd Used to filter all switching PAC pairs.
fisherThd	used to filter DE PAC list from DE/DEX method by pvalue<fisherThd.
logFCThd	used to filter |rcij| >=logFCThd, where |rcij| is the log2(ratio of PA1 between two samples/ratio of PA2).
selectOne	used only for method=DE/DEX, can be 'farest','logFC','fisherPV' to filter one switching pair.

Details

For linearTrend, switching events are not per-filtered by padj value, the change column (-1 or 1) is determined by cor value. For DE/DEX, it will first filter significant switching paris by fisherThd and logFCThd, and then select one pair by selectOne.

Value

A movUTRTrendRes object, having the following slots (type, method, group, conds, pairwise=list(padj, value), fullList) Here @fullList=[cond1.cond2, cond3.cond4, ...]. The full columns are: gene, nPAC, geneTag1, geneTag2, avgUTRlen1, avgUTRlen2, pvalue, padj, change <linear: cor, logRatio>, PAs1, PAs2.

See Also

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

Examples

data(PACds)
## Detect 3'UTR lengthening/shortening events using the linear trend method.
## Only PACs and genes with average read count between the two conditions >=10 and >=20 are used.
utr=movUTRtrend(PACds, group='group', method='linearTrend', avgPACtag=10, avgGeneTag=20)
## Number of genes for analyzing, including those not significant.
lapply(utr@fullList, nrow)
head(utr@fullList[["anther.embryo"]])
## Detect 3'UTR lengthening/shortening events using the DEX method.
## First get DE PAC results by DEXseq.
DEXPAC=movDEPAC(PACds, method='DEXseq', group='group', minSumPAT=10)
## Then get 3UTR switching events.
swDEX=movUTRtrend(PACds, group='group', method='DEX',
                  avgPACtag=10, avgGeneTag=20,
                  aMovDEPACRes=DEXPAC, DEPAC.padjThd=0.01,
                  mindist=50, fisherThd=0.01, logFCThd=1, selectOne='farest')
## Number of genes for analyzing, including those not significant.
lapply(swDEX@fullList, nrow)
head(swDEX@fullList[["anther.maturePollen"]])

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