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,
      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)

[Package ORFik version 1.10.13 Index]