windowPerReadLength {ORFik} | R Documentation

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

### Description

This is like a more detailed floss score, where floss score takes fraction of reads per read length over whole window, this is defined as: Fraction of reads per read length, per position in whole window (by upstream and downstream)

### 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"
    )

### 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` | any type of reads, usualy ribo seq. As GAlignment, GRanges or GRangesList object.
`pShifted` | a logical (TRUE), are riboseq reads p-shifted to size 1 width reads? If upstream and downstream is set, this argument is irrelevant.
`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), one of (zscore, transcriptNormalized, mean, median, sum, sumLength, fracPos), see ?coverageScorings. Use to decide a scoring of hits per position for metacoverage etc.

### Details

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.

### Value

a data.table with lengths by coverage / vector of proportions

### See Also

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

[Package ORFik version 1.6.9 Index]