readWidths {ORFik}R Documentation

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)

Arguments

reads

a GRanges or GAlignment object.

after.softclips

logical (TRUE), include softclips in width

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


[Package ORFik version 1.6.9 Index]