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 1.12.13 Index]