tallyBAM {h5vc} | R Documentation

## 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

### 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.

### 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.

### Author(s)

Paul Pyl

### 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

[Package h5vc version 2.20.0 Index]