mergeTallies {h5vc} | R Documentation

## 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

### 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.

### 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.

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

[Package h5vc version 2.18.0 Index]