systemPipeR (version 1.6.0)

alignStats: Alignment statistics

Description

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.

Usage

alignStats(args)

Arguments

args

Object of class SYSargs.

Value

data.frame with alignment statistics.

Examples

## 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)