windowPerGroup: Get window region of GRanges object

In JokingHero/ORFik: Open Reading Frames in Genomics

Get window region of GRanges object

Description

Per GRanges input (gr) of single position inputs (center point), create a GRangesList window output of specified upstream, downstream region relative to some transcript "tx".
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, it jumps to next exon.

Usage

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

Arguments

gr	a GRanges/IRanges object (startSites or others, must be single point per in genomic coordinates)
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, default (0), relative region to get upstream end from. (0 means start site, +1 is one upstream, -1 is one downstream)
downstream	an integer, default (0), relative region to get downstream end from (0 means start site, +1 is one downstream, -1 is one upstream)

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 useful for things like countOverlaps, since 0 hits will then always be returned for the correct object index. If you don't want the 0 width windows, use reduce() to remove 0-width windows.

Value

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

See Also

Other ExtendGenomicRanges: asTX(), coveragePerTiling(), extendLeaders(), extendTrailers(), 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 = 0, downstream = 0) # <- TIS
windowPerGroup(ORF, tx, upstream = 0, downstream = 1) # <- first and second base
windowPerGroup(ORF, tx, upstream = -1, downstream = 1) # <- second base
# find 2nd codon of an ORF on a spliced transcript
windowPerGroup(ORF, tx, upstream = -3, downstream = 5) # <- 2nd codon

# With multiple extensions downstream
ORF <- rep(ORF, 2)
names(ORF)[2] <- "tx1_2"
windowPerGroup(ORF, tx, upstream = 0, downstream = c(2, 5))
# The last one gives 2nd for first ORF and (1st and 2nd) codon for
# second ORF, returned as two groups of class GRanges/GRangsList

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.