Find overlaps between two GRangesList objects
findOverlapsGRL( GRL1, GRL2, annoName1 = "name", annoName2 = "name", check_names = TRUE, ... )
GRL1 | GRangesList query |
---|---|
GRL2 | GRangesList subject |
annoName1 | character value indicating either the colname of
|
annoName2 | character value indicating either the colname of
|
check_names | logical indicating whether the values defined
by |
... | additional arguments are passed to
|
Hits object, or the natural output from
GenomicRanges::findOverlaps()
dependent upon the ...
arguments,
subsetted for only entries with matching values defined
by annoName1
and annoName2
.
This function implements GenomicRanges::findOverlaps()
for the special
case of two GRangesList objects, restricting results to those including
the same GRangesList index in the subject and query.
Other jam GRanges functions:
addGRLgaps()
,
addGRgaps()
,
annotateGRLfromGRL()
,
annotateGRfromGR()
,
assignGRLexonNames()
,
closestExonToJunctions()
,
combineGRcoverage()
,
exoncov2polygon()
,
flattenExonsBy()
,
getFirstStrandedFromGRL()
,
getGRLgaps()
,
getGRcoverageFromBw()
,
getGRgaps()
,
grl2df()
,
jam_isDisjoint()
,
make_ref2compressed()
,
sortGRL()
,
spliceGR2junctionDF()
,
stackJunctions()
Other jam GRanges functions:
addGRLgaps()
,
addGRgaps()
,
annotateGRLfromGRL()
,
annotateGRfromGR()
,
assignGRLexonNames()
,
closestExonToJunctions()
,
combineGRcoverage()
,
exoncov2polygon()
,
flattenExonsBy()
,
getFirstStrandedFromGRL()
,
getGRLgaps()
,
getGRcoverageFromBw()
,
getGRgaps()
,
grl2df()
,
jam_isDisjoint()
,
make_ref2compressed()
,
sortGRL()
,
spliceGR2junctionDF()
,
stackJunctions()