reduceKeepAttr {ORFik} | R Documentation |
Extends function reduce
by trying to keep names and meta columns, if it is a
GRangesList. It also does not lose sorting for GRangesList,
since original reduce sorts all by ascending.
If keep.names == FALSE, it's just the normal GenomicRanges::reduce
with sorting negative strands descending for GRangesList.
reduceKeepAttr(grl, keep.names = FALSE, drop.empty.ranges = FALSE, min.gapwidth = 1L, with.revmap = FALSE, with.inframe.attrib = FALSE, ignore.strand = FALSE)
grl |
a |
keep.names |
(FALSE) keep the names and meta columns of the GRangesList |
drop.empty.ranges |
(FALSE) if a group is empty (width 0), delete it. |
min.gapwidth |
(1L) how long gap can it be to say they belong together |
with.revmap |
(FALSE) return info on which mapped to which |
with.inframe.attrib |
(FALSE) For internal use. |
ignore.strand |
(FALSE), can different strands be reduced together. |
A reduced GRangesList
Other ExtendGenomicRanges: asTX
,
coveragePerTiling
,
overlapsToCoverage
, tile1
,
txSeqsFromFa
, windowPerGroup
ORF <- GRanges(seqnames = "1", ranges = IRanges(start = c(1, 2, 3), end = c(1, 2, 3)), strand = "+") # For GRanges reduceKeepAttr(ORF, keep.names = TRUE) # For GRangesList grl <- GRangesList(tx1_1 = ORF) reduceKeepAttr(grl, keep.names = TRUE)