readWidths: Get read widths

In Roleren/ORFik: Open Reading Frames in Genomics

Get read widths

Description

Input any reads, e.g. ribo-seq object and get width of reads, this is to avoid confusion between width, qwidth and meta column containing original read width.

Usage

readWidths(reads, after.softclips = TRUE, along.reference = FALSE)

Arguments

reads	a GRanges, GAlignment, GAlignmentPairs or covRleList object.
after.softclips	logical (TRUE), include softclips in width. Does not apply if along.reference is TRUE.
along.reference	logical (FALSE), example: The cigar "26MI2" is by default width 28, but if along.reference is TRUE, it will be 26. The length of the read along the reference. Also "1D20M" will be 21 if by along.reference is TRUE. Intronic regions (cigar: N) will be removed. So: "1M200N19M" is 20, not 220.

Details

If input is p-shifted and GRanges, the "$size" or "$score" colum" must exist, and the column must contain the original read widths. In ORFik "$size" have higher priority than "$score" for defining length. ORFik P-shifting creates a $size column, other softwares like shoelaces creates a score column.

Remember to think about how you define length. Like the question: is a Illumina error mismatch sufficient to reduce size of read and how do you know what is biological variance and what are Illumina errors?

Value

an integer vector of widths

Examples

gr <- GRanges("chr1", 1)
readWidths(gr)

# GAlignment with hit (1M) and soft clipped base (1S)
ga <- GAlignments(seqnames = "1", pos = as.integer(1), cigar = "1M1S",
 strand = factor("+", levels = c("+", "-", "*")))
readWidths(ga) # Without soft-clip bases

readWidths(ga, after.softclips = FALSE) # With soft-clip bases

Roleren/ORFik documentation built on Oct. 19, 2024, 7:37 a.m.