windowPerGroup {ORFik}R Documentation

Get window region of GRanges object

Description

If downstream is 20, it means the window will start 20 downstream of gr start site (-20 in relative transcript coordinates.) If upstream is 20, it means the window will start 20 upstream of gr start site (+20 in relative transcript coordinates.) It will keep exon structure of tx, so if -20 is on next exon, the previous exon is of course deleted.

Usage

windowPerGroup(gr, tx, upstream = 0L, downstream = 0L)

Arguments

gr

a GRanges object (startSites and others, must be single point)

tx

a GRangesList of transcripts or (container region), names of tx must contain all gr names. The names of gr can also be the ORFik orf names. that is "txName_id"

upstream

an integer (0), relative region to get upstream from.

downstream

an integer (0), relative region to get downstream from

Details

If a region has a part that goes out of bounds, E.g if you try to get window around the CDS start site, goes longer than the 5' leader start site, it will set start to the edge boundary (the TSS of the transcript in this case). If region has no hit in bound, a width 0 GRanges object is returned. This is usefull for things like countOverlaps, since 0 hits will then always be returned for the correct object. If you don't want the 0 width windows, use reduce()

Value

a GRanges, or GRangesList object if any group had > 1 exon.

See Also

Other ExtendGenomicRanges: asTX, coveragePerTiling, overlapsToCoverage, reduceKeepAttr, tile1, txSeqsFromFa

Examples

# find 2nd codon of an ORF on a spliced transcript
ORF <- GRanges("1", c(3), "+") # start site
names(ORF) <- "tx1_1" # ORF 1 on tx1
tx <- GRangesList(tx1 = GRanges("1", c(1,3,5,7,9,11,13), "+"))
windowPerGroup(ORF, tx, upstream = -3, downstream = 5) # <- 2nd codon


[Package ORFik version 1.4.0 Index]