metaWindow {ORFik}R Documentation

Calculate meta-coverage of reads around input GRanges/List object.

Description

Sums up coverage over set of GRanges objects as a meta representation.

Usage

metaWindow(x, windows, scoring = "sum", withFrames = FALSE,
  zeroPosition = NULL, scaleTo = 100, returnAs = "data.frame",
  fraction = NULL, feature = NULL,
  forceUniqueEven = !is.null(scoring))

Arguments

x

GRangesList/GRanges object of your reads. Remember to resize them beforehand to width of 1 to focus on 5' ends of footprints, if that is wanted.

windows

GRangesList or GRanges of your ranges

scoring

a character, one of (zscore, transcriptNormalized, mean, median, sum, sumLength, NULL), see ?coverageScorings

withFrames

a logical (TRUE), return positions with the 3 frames, relative to zeroPosition. zeroPosition is frame 0.

zeroPosition

an integer DEFAULT (NULL), the point if all windows are equal size, that should be set to position 0. Like leaders and cds combination, then 0 is the TIS and -1 is last base in leader. NOTE!: if windows have different widths, this will be ignored.

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, sum(2,3)) etc.

returnAs

a character (data.frame), do data.table for speed.

fraction

a character/integer (NULL), the fraction i.e (27) for read length 27, or ("LSU") for large sub-unit TCP-seq.

feature

a character string, info on region. Usually either gene name, transcript part like cds, leader, or CpG motifs etc.

forceUniqueEven,

a logical (TRUE), require that all windows are of same width and even. To avoid bugs.

Value

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

See Also

Other coverage: coverageScorings, scaledWindowPositions, windowPerReadLength

Examples

library(GenomicRanges)
windows <- GRangesList(GRanges("chr1", IRanges(c(50, 100), c(80, 200)),
                               "-"))
x <- GenomicRanges::GRanges(
  seqnames = "chr1",
  ranges =  IRanges::IRanges(c(100, 180), c(200, 300)),
  strand = "-")
metaWindow(x, windows, withFrames = FALSE)


[Package ORFik version 1.4.0 Index]