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]