alignStats {systemPipeR} | R Documentation

## 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)

[Package systemPipeR version 2.0.8 Index]