windowPerGroup {ORFik} | R Documentation

## 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 from.
`downstream` | an integer, default (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 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 = -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 and (1st and 2nd) codon as two groups

[Package ORFik version 1.14.7 Index]