alignStats: Alignment statistics

In tgirke/systemPipeR: systemPipeR: Workflow Environment for Data Analysis and Report Generation

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, fqpaths, pairEnd = TRUE, output_index = 1, subset="FileName1")

Arguments

args	Object of class SYSargs or SYSargs2 or named character vector with BAM files PATH and the elements names should be the sampleID.
fqpaths	named character vector with raw FASTQ files PATH and the names should be the sampleID. Required when class(args) is "character".
pairEnd	logical. For pair-end libraries, select TRUE.
output_index	A numeric index positions of the file in SYSargs2 object, slot output. Default is output_index=1.
subset	subset are the variables defined in the param.yml file, for example "FileName1".

Value

data.frame with alignment statistics.

Author(s)

Thomas Girke

See Also

clusterRun and runCommandline and output_update

Examples

##########################################
## Examples with \code{SYSargs2} object ##
##########################################
## Construct SYSargs2 object from CWl param, CWL input, and targets files 
targetspath <- system.file("extdata", "targets.txt", package="systemPipeR")
dir_path <- system.file("extdata/cwl", package="systemPipeR")
WF <- loadWorkflow(targets=targetspath, wf_file="hisat2/hisat2-mapping-se.cwl", 
                  input_file="hisat2/hisat2-mapping-se.yml", dir_path=dir_path)
WF <- renderWF(WF, inputvars=c(FileName="_FASTQ_PATH1_", SampleName="_SampleName_"))
WF

names(WF); modules(WF); targets(WF)[1]; cmdlist(WF)[1:2]; output(WF)

## Not run: 
## Execute SYSargs2 on single machine
WF <- runCommandline(args=WF, make_bam=TRUE)

## Alignment stats
read_statsDF <- alignStats(WF, subset="FileName") 
write.table(read_statsDF, "results/alignStats.xls", row.names=FALSE, quote=FALSE, sep="\t")

## End(Not run)

#########################################
## Examples with \code{SYSargs} object ##
#########################################
## Construct SYSargs object from param and targets files 
param <- system.file("extdata", "hisat2.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) 
write.table(read_statsDF, "results/alignStats.xls", row.names=FALSE, quote=FALSE, sep="\t")

## End(Not run)

tgirke/systemPipeR documentation built on Sept. 24, 2024, 9:48 a.m.