h5vc (version 2.6.3)

mergeTallies: Merging the prepared results from multiple bam file tallies into one block that can be written to the HDF5 tally file

Description

This function merges a set of tallies that have been processed with prepareForHDF5 into one block of data.

Usage

mergeTallies( tallies )

Arguments

tallies

A list of prepared talies, i.e. a list of lists with slots for the datasets "Counts", "Coverage", "Deletions" and "Reference" in each sub-list

Value

• A list with slots containing the Counts,Coverages,Deletions and Reference datasets for the samples given in tallies. Each of the slots contains an array with the contents of the provided sub-lists merged along the "sample" axis. The Reference slot os filled from the first element of tallies and it is up to the user to make sure that the tallies provided for merging have compatible references.

Details

This function merges tallies from a set of bam files / samples, note that the order of samples in the sample column will be the same as the order of samples in the provided list, so ake sure this matches your sampledata.

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(bamf, chrom, startpos, endpos) } )
str(theData)
reference <- getSeq(BSgenome.Hsapiens.UCSC.hg19, "chr1", startpos, endpos)
theMergedData <- mergeTallies(lapply(theData, prepareForHDF5, reference))
str(theMergedData)