movStat: Make statistics for a object

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

Make statistics for a object

Description

movStat(object) makes statistics for a movRes or PACdataset object. It is a generic function to make statistics of a object which is normally of movRes or PACddataset class.

movStat(movRes) makes statistics for a movRes object.

movStat(PACdataset) makes statistics for a PACdataset object.

Usage

movStat(object, ...)

## S4 method for signature 'movRes'
movStat(object, padjThd = NULL, valueThd = NULL, upThd = NULL, dnThd = NULL)

## S4 method for signature 'PACdataset'
movStat(object, minPAT = c(1, 5, 10), ofilePrefix = NULL)

Arguments

object	Normally a movRes or PACdataset object.
...	Arguments passing to other functions.
padjThd	cutoff to filter rows with aMovRes@pairwise$padj<padjThd.
valueThd	cutoff to filter rows with aMovRes@pairwise$value|>=valueThd.
upThd	cutoff to filter up-regulated rows with aMovRes@pairwise$value>=upThd.
dnThd	cutoff to filter down-regulated rows with aMovRes@pairwise$value<=dnThd.
minPAT	min PAT number to filter valid PACs with expression level >= minPAT, can be like 5 or c(5,10)
ofilePrefix	output stat results to a txt file named <ofilePrefix.patX.stat>. If it is NULL, then do not output to file.

Details

Statistical results of movStat(movRes) are numbers of significant DE genes/PACs/switching events, the significant gene/PAC list for each condition pair, etc.

Statistical results of movStat(PACdataset) are the distributions PATs, PACs etc.

Value

A list of several data frames including nsig, siglist, tf01, ovp, de01, and deNum.

A list of data frames representing results from different cutoffs like [PAT1, PAT5, PAT10]. Each item is a data frame recording statistical results.

Methods (by class)

• movStat(movRes): for a movRes object.

• movStat(PACdataset): for a PACdataset object.

See Also

plotPACdsStat for plot the stat results of PACdataset.

Other mov-like functions: movSelect()

Examples

## movStat(PACdataset) ##
data(PACds)
## Stat a PACds, filtering PACs with cutoffs of 1, 5, and 10.
pstats=movStat(PACds, minPAT=c(1,5,10), ofilePrefix='statFileEach')

## If the PACds includes replicates, you may want to pool replicates first and then make stats.
pstats=movStat(subsetPACds(PACds, group='group', pool=TRUE),
              minPAT=c(1,5,10), ofilePrefix='statFilePool')

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