scaledWindowPositions {ORFik}R Documentation

Scale windows to a meta window of size

Description

For example scale a coverage plot of a all human CDS to width 100

Usage

scaledWindowPositions(grl, reads, scaleTo = 100, scoring = "meanPos")

Arguments

grl

GRangesList or GRanges of your ranges

reads

GRanges object of your reads.

scaleTo

an integer (100), if windows have different size, a meta window can not directly be created, since a meta window must have equal size for all windows. Rescale all windows to scaleTo. i.e c(1,2,3) -> size 2 -> c(1, mean(2,3)) etc. Can also be a vector, 1 number per grl group.

scoring

a character, one of (meanPos, sumPos)

Details

Nice for making metaplots, the score will be mean of merged positions.

Value

A data.table with scored counts (counts) of reads mapped to positions (position) specified in windows along with frame (frame).

See Also

Other coverage: coverageScorings, metaWindow, windowPerReadLength

Examples

library(GenomicRanges)
windows <- GRangesList(GRanges("chr1", IRanges(1, 200), "-"))
x <- GenomicRanges::GRanges(
  seqnames = "chr1",
  ranges =  IRanges::IRanges(c(1, 100, 199), c(2, 101, 200)),
  strand = "-")
scaledWindowPositions(windows, x, scaleTo = 100)


[Package ORFik version 1.4.0 Index]