h5vc (version 2.6.3)

tallyBAM: tallyBAM

Description

Function for creating tallies from bam files.

Usage

tallyBAM(file, chr, start, stop, q=25, ncycles = 0, max.depth=1000000, verbose=FALSE, reference = NULL)

Arguments

file

filename of the BAM file that should be tallies

chr

Chromosome in which to tally

start

First position of the tally

stop

Last position of the tally

q

quality cut-off for considering a base call

ncycles

number of sequencing cycles form the front and back of the read that should be considered unreliable

max.depth

only tally a position if there are less than this many reads overlapping it - can prevent long runtimes in unreliable regions

verbose

should additional information be printed

reference

DNAString object holding the reference sequence of the region being tallies, if this is NULL (the default) the raw tally is returned, otherwise prepareForHDF5 is called with the raw tally and the reference and the prepared tally is returned instead

Value

• An array object with dimensions [stop - start + 1, 18, 2] which represent positions times nucleotides (4 bases + deletions + insertions times three for early, middle and late sequencing cycles) times strands.

Details

This function tallies nucleotides and deletion counts in the specified region of a given BAM file. The results can be processed with the prepareForHDF5 function. This function was adapted from the bam2R function provided by the deepSNV package.

Examples

library(h5vc)
files <- c("NRAS.AML.bam","NRAS.Control.bam")
bamFiles <- file.path( system.file("extdata", package = "h5vcData"), files)
chrom = "1"
startpos <- 115247090
endpos <- 115259515
theData <- lapply( bamFiles, function(bamf){
  tallyBAM( file = bamf, chr = chrom, start = startpos, stop = endpos, ncycles = 10 )
})
str(theData)
print(theData[[1]][,,,9491]) #position 9491 of the pileup