read.bam: Reads a BAM file using the Rsamtools package and manipulates...

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

Description

The read.bam function reads all alignments between two points from a particular chromosome/reference sequence. A variety of manipulations are performed, including conversion of the read data into a data.frame.

Usage

read.bam(bamfile = NULL, chr = NULL, start = 1, end = 1e+07, what = c("qname", "flag", "rname", "strand", "pos", "qwidth", "mapq", "cigar", "mrnm", "mpos", "isize", "seq"), tag = c("NM"), removeN = TRUE)

Arguments

bamfile	Full path to the indexed BAM file
chr	The name of the chromosome from which alignments should be extracted
start	The start position from which alignments should be extracted
end	The end position from which alignments should be extracted
what	A vector of column names to be extracted. See scanBamWhat. At present allowed values are any subset of c("qname","flag","rname","strand","pos","qwidth","mapq","cigar","mrnm","mpos","isize","seq","qual"). We recommend sticking with the default.
tag	Tags to be exctracted from the BAM file. See scanBam. Many different tags are used by the various aligners that exist, and we recommend referring to the manual of your chosen aligner to discover which tags are used, and which you may find useful.
removeN	Logical. Whether or not to remove all sequences that contain Ns

Details

A wrapper around scanBam to read in a subset of aliignments from a BAM file and return those as a data.frame.

Value

A data frame with reads/alignments as rows and columns defined by the "what" and "tag" columns.

Author(s)

Mick Watson

See Also

scanBam, clip.bam

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: bam[1:10,]

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