systemPipeR (version 1.6.0)

mergeBamByFactor: Merge BAM files based on factor

Description

Merges BAM files based on sample groupings provided by a factor using internally the mergeBam function from the Rsamtools package. The function also returns an updated SYSargs object containing the paths to the merged BAM files as well as to the unmerged BAM files if there are any. All rows of merged parent samples are removed.

The functionality provided by mergeBamByFactor is useful for experiments where pooling of replicates is advantageous to maximize the depth of read coverage, such as prior to peak calling in ChIP-Seq or miRNA gene prediction experiments.

Usage

mergeBamByFactor(args, mergefactor = targetsin(args)$Factor, overwrite = FALSE, silent = FALSE, ...)

Arguments

args

An instance of SYSargs constructed from a targets file where the first column (targetsin(args)) contains the paths to the BAM files along with the column title FileName.

mergefactor

factor containing the grouping information required for merging the BAM files referenced in the first column of targetsin(args). The default uses targetsin(args)$Factor as factor. The latter merges BAM files for which replicates are specified in the Factor column.

overwrite

If overwrite=FALSE existing BAM files of the same name will not be overwritten.

silent

If silent=TRUE print statements will be suppressed.

...

To pass on additional arguments to the internally used mergeBam function from Rsamtools.

Value

The merged BAM files will be written to output files with the following naming convention: _.. In addition, the function returns an updated SYSargs object where all output file paths contain the paths to the merged BAM files. The rows of the merged parent samples are removed and the rows of the unmerged samples remain unchanged.

See Also

writeTargetsout, writeTargetsRef

Examples

## Construct initial SYSargs object
targetspath <- system.file("extdata", "targets_chip.txt", package="systemPipeR")
parampath <- system.file("extdata", "bowtieSE.param", package="systemPipeR")
args <- systemArgs(sysma=parampath, mytargets=targetspath)

## Not run: 
# ## After running alignmets (e.g. with Bowtie2) generate targets file 
# ## for the corresponding BAM files. The alignment step is skipped here.
# writeTargetsout(x=args, file="targets_bam.txt", overwrite=TRUE) 
# args <- systemArgs(sysma=NULL, mytargets="targets_bam.txt")
# 
# ## Merge BAM files and return updated SYSargs object
# args_merge <- mergeBamByFactor(args, overwrite=TRUE, silent=FALSE)
# 
# ## Export modified targets file 
# writeTargetsout(x=args_merge, file="targets_mergeBamByFactor.txt", overwrite=TRUE) 
# ## End(Not run)