alignStats {systemPipeR} | R Documentation |
Generate data frame containing important read alignment statistics such as the total number of reads in the FASTQ files, the number of total alignments, as well as the number of primary alignments in the corresponding BAM files.
alignStats(args)
args |
Object of class |
data.frame
with alignment statistics.
Thomas Girke
## Construct SYSargs object from param and targets files param <- system.file("extdata", "tophat.param", package="systemPipeR") targets <- system.file("extdata", "targets.txt", package="systemPipeR") args <- systemArgs(sysma=param, mytargets=targets) args names(args); modules(args); cores(args); outpaths(args); sysargs(args) ## Not run: ## Execute SYSargs on single machine runCommandline(args=args) ## Execute SYSargs on multiple machines qsubargs <- getQsubargs(queue="batch", Nnodes="nodes=1", cores=cores(tophat), memory="mem=10gb", time="walltime=20:00:00") qsubRun(args=args, qsubargs=qsubargs, Nqsubs=1, package="systemPipeR") ## Alignment stats read_statsDF <- alignStats(args) read_statsDF <- cbind(read_statsDF[targets$FileName,], targets) write.table(read_statsDF, "results/alignStats.xls", row.names=FALSE, quote=FALSE, sep="\t") ## End(Not run)