scaledWindowPositions: Scale (bin) windows to a meta window of given size
In ORFik: Open Reading Frames in Genomics

Description Usage Arguments Details Value See Also Examples

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

scaledWindowPositions(
  grl,
  reads,
  scaleTo = 100,
  scoring = "meanPos",
  weight = "score",
  is.sorted = FALSE
)

`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)
`weight`	(default: 'score'), if defined a character name of valid meta column in subject. GRanges("chr1", 1, "+", score = 5), would mean score column tells that this alignment region was found 5 times. ORFik .bedo files, contains a score column like this. As do CAGEr CAGE files and many other package formats. You can also assign a score column manually.
`is.sorted`	logical (FALSE), is grl sorted. That is + strand groups in increasing ranges (1,2,3), and - strand groups in decreasing ranges (3,2,1)

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

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

Other coverage: coverageScorings(), metaWindow(), regionPerReadLength(), windowPerReadLength()

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)