windowPerReadLength: Find proportion of reads per position per read length in...

In ORFik: Open Reading Frames in Genomics

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")

ORFik documentation built on March 27, 2021, 6 p.m.