prepareForHDF5 {h5vc}R Documentation

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

Details

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

Value

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

Author(s)

Paul Pyl

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)
[Package h5vc version 2.20.0 Index]