h5vc (version 2.6.3)

prepareForHDF5: Preparing the results of tallyBAM for writing to an HDF5 tally file

Description

This function prepares the resulting array of a call to tallyBAM for writing to an HDF5 tally file.

Usage

prepareForHDF5( counts, reference )

Arguments

counts

An array as produced by a call to tallyBAM

reference

A DNAString object containing the reference sequence corresponding to the region that is described in the counts array -- if this is NULL a consensus vote will be used to estimate the reference at any given position, this means you cannot detect variants with AF >= 0.5 anymore

Value

• A list with slots containing the Counts,Coverages,Deletions and Reference datasets for the given sample.

Details

This function performs the neccessary transformation to the array returned by tallyBAM to be compatible with the HDF5 tally file data structure.

Examples

library(h5vc)
library(BSgenome.Hsapiens.UCSC.hg19)
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 )
})
reference <- getSeq(BSgenome.Hsapiens.UCSC.hg19, "chr1", startpos, endpos)
theData <- lapply(theData, prepareForHDF5, reference)
str(theData)