scaledWindowPositions {ORFik}R Documentation

Scale (bin) windows to a meta window of given size

Description

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

Usage

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

Arguments

grl

a GRangesList of 5' utrs, CDS, transcripts, etc.

reads

a GAlignments or GRanges object of RiboSeq, RnaSeq etc. Weigths for scoring is default the 'score' column in '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, ..) Check the coverageScoring function for more options.

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 ofst, bedoc and .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)

drop.zero.dt

logical FALSE, if TRUE and as.data.table is TRUE, remove all 0 count positions. This greatly speeds up and most importantly, greatly reduces memory usage. Will not change any plots, unless 0 positions are used in some sense. (mean, median, zscore coverage will only scale differently)

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(), regionPerReadLength(), 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 1.13.14 Index]