regionPerReadLength: Find proportion of reads per position per read length in...
In ORFik: Open Reading Frames in Genomics

Description Usage Arguments Value See Also Examples

This is defined as: Given some transcript region (like CDS), get coverage per position.

regionPerReadLength(
  grl,
  reads,
  acceptedLengths = NULL,
  withFrames = TRUE,
  scoring = "transcriptNormalized",
  weight = "score",
  BPPARAM = bpparam()
)

`grl`	a `GRangesList` object with usually either leaders, cds', 3' utrs or ORFs
`reads`	a `GAlignments` or `GRanges` object of RiboSeq, RnaSeq etc. Weigths for scoring is default the 'score' column in 'reads'
`acceptedLengths`	an integer vector (NULL), the read lengths accepted. Default NULL, means all lengths accepted.
`withFrames`	logical TRUE, add ORF frame (frame 0, 1, 2), starting on first position of every grl.
`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.
`BPPARAM`	how many cores/threads to use? default: bpparam()

a data.table with lengths by coverage.

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

# Raw counts per gene per position
cds <- GRangesList(tx1 = GRanges("1", 100:129, "+"))
reads <- GRanges("1", seq(79,129, 3), "+")
reads$size <- 28 # <- Set read length of reads
regionPerReadLength(cds, reads, scoring = NULL)
## Sum up reads in each frame per read length per gene
regionPerReadLength(cds, reads, scoring = "frameSumPerLG")