deepSNV (version 1.18.3)

bam2R: Read nucleotide counts from a .bam file

Description

This function uses a C interface to read the nucleotide counts on each position of a .bam alignment. The counts of both strands are reported separately and nucleotides below a quality cutoff are masked. It is called by deepSNV to parse the alignments of the test and control experiments, respectively.

Usage

bam2R(file, chr, start, stop, q = 25, s = 2, head.clip = 0, max.depth = 1e+06, verbose = FALSE)

Arguments

file

The name of the .bam file as a string.

chr

The chromosome as a string.

start

The start position (1-indexed).

stop

The end position (1-indexed).

q

An optional cutoff for the nucleotide Phred quality. Default q = 25. Nucleotides with Q < q will be masked by 'N'.

s

Optional choice of the strand. Defaults to s = 2 (both).

head.clip

Should n nucleotides from the head of reads be clipped? Default 0.

max.depth

The maximal depth for the pileup command. Default 1,000,000.

verbose

Boolean. Set to TRUE if you want to get additional output.

Value

A named matrix with rows corresponding to genomic positions and columns for the nucleotide counts (A, T, C, G, -), masked nucleotides (N), (INS)ertions, (DEL)etions, (HEAD)s and (TAIL)s that count how often a read begins and ends at the given position, respectively, and the sum of alignment (QUAL)ities, which can be indicative of alignment problems. Counts from matches on the reference strand (s=0) are uppercase, counts on the complement (s=1) are lowercase. The returned matrix has 11 * 2 (strands) = 22 columns and (stop - start + 1) rows.

Examples

## Simple example:
counts <- bam2R(file = system.file("extdata", "test.bam", package="deepSNV"), chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 3120, stop=3140, q = 10)
show(counts)
## Not run: Requires an internet connection, but try yourself.
# bam <- bam2R(file = "http://www.bsse.ethz.ch/cbg/software/deepSNV/data/test.bam", chr="B.FR.83.HXB2_LAI_IIIB_BRU_K034", start = 2074, stop=3585, q=10)
# head(bam)