sequence.report: Produce a summary of the entire BAM alignment, grouped by...

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

Description

For the positive and negative strand, group the data by reference, position, sequence length and strand and count the occurrence, producing a data.frame. Basically counts the occurrence of each unique read/mapping location.

Usage

sequence.report(df = NULL, minlen = 1, maxlen = 37)

Arguments

df	A data.frame as output by read.bam and clip.bam
minlen	The minimum length of reads/alignments to include
maxlen	The maximum length of reads/alignments to include

Value

A data.frame with columns:

ref	The name of the reference sequence
pos	Position in the reference
strand	The strand
seq	The sequence of the aligned read
len	The length of the alignment
count	The count of the occurrence of this sequence at this location/strand

Author(s)

Mick Watson

Examples

 ## Not run: infile <- system.file("data/SRR389184_vs_SINV_sorted.bam", package="viRome")
 ## Not run: bam <- read.bam(bamfile=infile, chr="SINV", minlen=1, maxlen=12000, removeN=TRUE)
 ## Not run: bamc <- clip.bam(bam)
 ## Not run: sr <- sequence.report(bamc)
 ## Not run: sr

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