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

In ORFik: Open Reading Frames in Genomics

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,
  fraction = NULL,
  feature = NULL,
  forceUniqueEven = !is.null(scoring),
  forceRescale = TRUE,
  weight = "score"
)

Arguments

x	GRanges/GAlignment object of your reads. Remember to resize them beforehand to width of 1 to focus on 5' ends of footprints etc, if that is wanted.
windows	GRangesList or GRanges of your ranges
scoring	a character, default: "sum", one of (zscore, transcriptNormalized, mean, median, sum, sumLength, NULL), see ?coverageScorings for info and more alternatives.
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 (bin) all windows to scaleTo. i.e c(1,2,3) -> size 2 -> coverage of position c(1, mean(2,3)) etc.
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), if TRUE; require that all windows are of same width and even. To avoid bugs. FALSE if score is NULL.
forceRescale	logical, default TRUE. If TRUE, if unique(widthPerGroup(windows)) has length > 1, it will force all windows to width of the scaleTo argument, making a binned meta coverage.
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.

Value

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

See Also

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

ORFik documentation built on March 27, 2021, 6 p.m.