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]