findOvpPACds: Find overlapping PACdataset

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

Find overlapping PACdataset

Description

findOvpPACds returns overlapping PACdataset.

Usage

findOvpPACds(
  qryPACds,
  sbjPACds,
  qryMode = "point",
  sbjMode = "point",
  d = 0,
  qryPAT = 1,
  sbjPAT = 1,
  returnOvp = TRUE,
  returnNonOvp = FALSE,
  verbose = TRUE
)

Arguments

qryPACds	a query PACdataset, will subset and return the qryPACds.
sbjPACds	a subject PACdataset.
qryMode	use coord or UPA_start/UPA_end for qryPACds. Default is point (using coord), if qryMode=region, then use UPA_start/UPA_end.
sbjMode	same as qryMode except for sbjPACds.
d	distance to count overlapping, default is 0 (no gap between qry and sbj).
qryPAT	cutoff to filter qryPACds. If sbjPAT<=1, then do not filter.
sbjPAT	same as qryPAT but to filter sbjPACds.
returnOvp	default is TRUE; if TRUE then return overlapping qryPACds.
returnNonOvp	default is FALSE; if TRUE then return nonOverlapping qryPACds. If both returnOvp=T and returnNonOvp=TRUE, then return a list(ovp, nonOvp)
verbose	print information.

Details

This function is used to subset one PACds with another PACds.

Value

A subset PACdataset of qryPACds.

Examples

data(PACds)
pacds1=PACds
pacds2=PACds
pacds2@anno$coord=pacds2@anno$coord+sample(-10:10, 1)
## return overlapped qryPACds without filtering, comparing coord~coord
pd=findOvpPACds(qryPACds=pacds1, sbjPACds=pacds2, d=0, qryPAT=1, sbjPAT=1)
## return overlapped qryPACds with filtering, comparing coord~coord
pd=findOvpPACds(qryPACds=pacds1, sbjPACds=pacds2, d=50, qryPAT=1, sbjPAT=10)
## return overlapped qryPACds comparing qry's coord ~ sbj's UPA_start/end
pd=findOvpPACds(qryPACds=pacds1, sbjPACds=pacds2, d=0, qryMode='point', sbjMode='region')

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