mergeTallies: Merging the prepared results from multiple bam file tallies...
In h5vc: Managing alignment tallies using a hdf5 backend

Description Usage Arguments Details Value Author(s) Examples

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

1	mergeTallies( tallies )

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

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.

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.

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