Get gaps in GRangesList objects
getGRLgaps(grl, strandSpecific = TRUE, verbose = FALSE, ...)
| grl | GRangesList object. |
|---|---|
| strandSpecific | logical indicating whether to determine gaps within strand. |
| verbose | logical indicating whether to print verbose output. |
| ... | additional arguments are ignored. |
GRangesList object with gaps for each chromosome and strand present in each GRanges entry. It does not return gap sequence at the edges of GRanges regions to the chromosome ends.
This function returns gaps between GRanges regions in a GRangesList
object. When strandSpecific=TRUE is determines gaps per strand,
otherwise strands are converted to "*". It will also determine
gaps within chromosome for each GRanges entry in GRangesList.
Other jam GRanges functions:
addGRLgaps(),
addGRgaps(),
annotateGRLfromGRL(),
annotateGRfromGR(),
assignGRLexonNames(),
closestExonToJunctions(),
combineGRcoverage(),
exoncov2polygon(),
findOverlapsGRL(),
flattenExonsBy(),
getFirstStrandedFromGRL(),
getGRcoverageFromBw(),
getGRgaps(),
grl2df(),
jam_isDisjoint(),
make_ref2compressed(),
sortGRL(),
spliceGR2junctionDF(),
stackJunctions()