subsetPACds: Subset a PACdataset

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

Subset a PACdataset

Description

subsetPACds returns a subset of PACdataset.

Usage

subsetPACds(
  pacds,
  group = NULL,
  cond1 = NULL,
  cond2 = NULL,
  conds = NULL,
  avgPACtag = 0,
  avgGeneTag = 0,
  totPACtag = 0,
  choosePA = NULL,
  PAs = NULL,
  genes = NULL,
  chrs = NULL,
  noIntergenic = FALSE,
  avg = FALSE,
  pool = FALSE,
  clearPAT = 0,
  minExprConds = 1,
  verbose = FALSE
)

Arguments

pacds	A PACdataset object.
group	a sample group, must be present in PACds@colData. If NULL, then parameters of cond1, cond2, and avg are not in use.
cond1	a condition, must be present in PACds@colData.
cond2	a condition, must be present in PACds@colData. If cond1 or cond2 is NULL, then both cond1 and cond2 are set NULL.
conds	to subset multiple conditions.
avgPACtag	if >0, then filter PACs with average PAT number across all samples >= avgPACtag, after subseting by group and conds.
avgGeneTag	similar to avgPACtag, but for gene.
totPACtag	filter PACs with total PAT number of all samples >=totPACtag.
choosePA	value can e NULL/distal/proximal/APA. Only if PACds is all 3UTRAPA, then choosePA can be distal/proximal. APA means choose PACs from APA genes.
PAs	to filter PACs by a PAC name list according to rownames in PAs.
genes	to filter by a gene name list according to PACds@anno$gene.
chrs	to filter by a chr name list according to PACds@anno$chr.
noIntergenic	whether to remove intergenic PACs.
avg	TRUR/FALSE. If TRUE then take average of replicates of each of subset conditions.
pool	TRUR/FALSE. If TRUE then take pool value of replicates of each of subset conditions.
clearPAT	If >0 then set @counts[<=clearPAT]=0 and remove blank lines and reset PACds@anno.
minExprConds	default 1, min number of condtions (columns) expressed.
verbose	T to show message during subsetting.

Value

A subset of PACdataset with 0-count lines removed.

Examples

data(PACds)
PACds1=subsetPACds(PACds, group='group', pool=TRUE)
## Subset two conditions.
pacds=subsetPACds(PACds, group='group',cond1='anther', cond2='embryo')
## Subset PACs from APA genes in two conditions.
PACds1=subsetPACds(PACds, group='group', cond1='anther', cond2='embryo', choosePA='apa')
## Subset PACs of given genes.
subsetPACds(PACds, genes=PACds@anno$gene[1:5], verbose=TRUE)
## Subset PACs of given PA names.
swPAC=subsetPACds(PACds, PAs=rownames(PACds@counts)[1:5], verbose=TRUE)

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