windowPerReadLength {ORFik} | R Documentation

## Find proportion of reads per position per read length in window

### Description

This is defined as: Fraction of reads per read length, per position in whole window (defined by upstream and downstream) If tx is not NULL, it gives a metaWindow, centered around startSite of grl from upstream and downstream. If tx is NULL, it will use only downstream , since it has no reference on how to find upstream region. The exception is when upstream is negative, that is, going into downstream region of the object.

### Usage

    windowPerReadLength(
      grl,
      tx = NULL,
      reads,
      pShifted = TRUE,
      upstream = if (pShifted) 5 else 20,
      downstream = if (pShifted) 20 else 5,
      acceptedLengths = NULL,
      zeroPosition = upstream,
      scoring = "transcriptNormalized",
      weight = "score"
    )

### Arguments

`grl` | a `GRangesList` object with usually either leaders, cds', 3' utrs or ORFs
`tx` | default NULL, a GRangesList of transcripts or (container region), names of tx must contain all grl names. The names of grl can also be the ORFik orf names. that is "txName_id"
`reads` | a `GAlignments` or `GRanges` object of RiboSeq, RnaSeq etc. Weigths for scoring is default the 'score' column in 'reads'
`pShifted` | a logical (TRUE), are Ribo-seq reads p-shifted to size 1 width reads? If upstream and downstream is set, this argument is irrelevant. So set to FALSE if this is not p-shifted Ribo-seq.
`upstream` | an integer (5), relative region to get upstream from.
`downstream` | an integer (20), relative region to get downstream from
`acceptedLengths` | an integer vector (NULL), the read lengths accepted. Default NULL, means all lengths accepted.
`zeroPosition` | an integer DEFAULT (upstream), what is the center point? 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.
`scoring` | a character (transcriptNormalized), which meta coverage scoring ? one of (zscore, transcriptNormalized, mean, median, sum, sumLength, fracPos), see ?coverageScorings for more info. Use to decide a scoring of hits per position for metacoverage etc. Set to NULL if you do not want meta coverage, but instead want per gene per position raw counts.
`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 lengths by coverage / vector of proportions

### See Also

Other coverage: `coverageScorings()`, `metaWindow()`, `regionPerReadLength()`, `scaledWindowPositions()`

### Examples

    cds <- GRangesList(tx1 = GRanges("1", 100:129, "+"))
    tx <- GRangesList(tx1 = GRanges("1", 80:129, "+"))
    reads <- GRanges("1", seq(79,129, 3), "+")
    windowPerReadLength(cds, tx, reads, scoring = "sum")
    windowPerReadLength(cds, tx, reads, scoring = "transcriptNormalized")

[Package ORFik version 1.10.13 Index]