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, output_index = 1, subset="FileName1")
args |
Object of class |
output_index |
A numeric index positions of the file in |
subset |
|
data.frame
with alignment statistics.
Thomas Girke
clusterRun
and runCommandline
and output_update
######################################### ## Examples with \code{SYSargs} object ## ######################################### ## 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) ## Alignment stats read_statsDF <- alignStats(args) read_statsDF <- cbind(read_statsDF[targets$FileName,], targets) write.table(read_statsDF, "results/alignStats.xls", row.names=FALSE, quote=FALSE, sep="\t") ## End(Not run) ########################################## ## Examples with \code{SYSargs2} object ## ########################################## ## Construct SYSargs2 object from CWl param, CWL input, and targets files targets <- system.file("extdata", "targets.txt", package="systemPipeR") dir_path <- system.file("extdata/cwl/hisat2/hisat2-se", package="systemPipeR") WF <- loadWorkflow(targets=targets, wf_file="hisat2-mapping-se.cwl", input_file="hisat2-mapping-se.yml", dir_path=dir_path) WF <- renderWF(WF, inputvars=c(FileName="_FASTQ_PATH1_", SampleName="_SampleName_")) WF targets <- system.file("extdata", "targets.txt", package="systemPipeR") names(WF); modules(WF); targets(WF)[1]; cmdlist(WF)[1:2]; output(WF) ## Not run: ## Execute SYSargs2 on single machine WF <- runCommandline(args=WF) ## Alignment stats read_statsDF <- alignStats(WF) read_statsDF <- cbind(read_statsDF[targets$FileName,], targets) write.table(read_statsDF, "results/alignStats.xls", row.names=FALSE, quote=FALSE, sep="\t") ## End(Not run)