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]