summarise.by.length: Summarise reads mapped by length of the read and position in...

In mw55309/viRome_legacy: Analysis and visualisation of short-read sequencing data from virus-infection studies

Description

This function takes the results of read.bam and clip.bam and counts the occurrence of the length of reads mapping to each position in the reference genome

Usage

summarise.by.length(vdf = NULL, minlen = 1, maxlen = 37, start = 1, end = 1e+07, strand = NULL)

Arguments

vdf	the results of read.bam and clip.bam
minlen	The minimum length of aligned read to consider
maxlen	The maximum length of aligned read to consider
start	The start position from which alignments should be extracted
end	The end position from which alignments should be extracted
strand	Choose which strand to count reads on. One of either "pos" or "neg". For both strands, set to NULL (the default).

Value

The result is a data.frame, the columns being read lengths, the rows being position in the genome, and the values being counts.

Author(s)

Mick Watson <[e-mail]>

Examples

 ## Not run: infile <- system.file("data/SRR389184_vs_SINV_sorted.bam", package="viRome")
 ## Not run: bam <- read.bam(bamfile=infile, chr="SINV", start=1, end=11703, removeN=TRUE)
 ## Not run: bamc <- clip.bam(bam)
## Not run: dm <- summarise.by.length(bamc)
## Not run: dmp <- summarise.by.length(bamc, strand="pos")
## Not run: dmn <- summarise.by.length(bamc, strand="neg")

mw55309/viRome_legacy documentation built on Dec. 21, 2021, 11:05 p.m.