readWidths {ORFik} | R Documentation

## Get RiboSeq widths

### Description

Input a 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 (FALSE), include softclips in width

### Details

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

### 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 1.4.1 Index]