prepareForHDF5 {h5vc} | R Documentation |
This function prepares the resulting array of a call to tallyBAM
for writing to an HDF5 tally file.
prepareForHDF5( counts, reference )
counts |
An array as produced by a call to |
reference |
A DNAString object containing the reference sequence corresponding to the region that is described in the counts array – if this is |
This function performs the neccessary transformation to the array
returned by tallyBAM
to be compatible with the HDF5 tally file data structure.
A list with slots containing the Counts
,Coverages
,Deletions
and Reference
datasets for the given sample.
Paul Pyl
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)