readWidths {ORFik} | R Documentation |
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.
readWidths(reads, after.softclips = TRUE)
reads |
a GRanges or GAlignment object. |
after.softclips |
logical (TRUE), include softclips in width |
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?
an integer vector of widths
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