qa {ShortRead} | R Documentation

## Perform quality assessment on short reads

### Description

This function is a common interface to quality assessment functions available in `ShortRead`. Results from this function may be displayed in brief, or integrated into reports using, e.g., `report`.

### Usage

    qa(dirPath, ...)
    ## S4 method for signature 'character'
    qa(dirPath, pattern=character(0),
        type=c("fastq", "SolexaExport", "SolexaRealign", "Bowtie",
               "MAQMap", "MAQMapShort"),
        ...)
    ## S4 method for signature 'list'
    qa(dirPath, ...)

### Arguments

`dirPath` | A character vector or other object (e.g., `SolexaPath`; see `showMethods`, below) locating the data for which quality assessment is to be performed. See help pages for defined methods (by evaluating the example code, below) for details of available methods.
`pattern` | A character vector limiting the files in `dirPath` to be processed, as with `list.files`. Care should be taken to specify pattern to avoid reading unintended files.
`type` | The type of file being parsed; must be a character vector of length 1, selected from one of the types enumerated in the parameter.
`...` | Additional arguments used by methods. `sample=TRUE`: Logical(1) indicating whether QA should be performed on a sample (default size 1000000) drawn from each FASTQ file, or from the entire file. `n`: The number of reads to sample when processing FASTQ files. `Lpattern`, `Rpattern`: A character vector or XString object to be matched to the left end of a sequence. If either `Lpattern` or `Rpattern` are provided, `trimLRPatterns` is invoked to produce a measure of adapter contamination. Mismatch rates are 0.1 on the left and 0.2 on the right, with a minimum overlap of 10 nt. `BPPARAM`: How parallel evalutation will be performed. see `BiocParallelParam`; the default is `BiocParallel::registered()[1]`.

### Details

The most common use of this function provides a directory path and pattern identifying FASTQ files for quality assessment. The default is then to create a quality assessment report based on a random sample of n=1000000 reads from each file.

The following methods are defined, in addition to those on S4 formal classes documented elsewhere:

`qa,character-method`

  Quality assessment is performed on all files in directory `dirPath` whose file name matches `pattern`. The type of analysis performed is based on the `type` argument. Use `SolexaExport` when all files matching `pattern` are Solexa `_export.txt` files. Use `SolexaRealign` for Solexa `_realign.txt` files. Use `Bowtie` for Bowtie files. Use `MAQMapShort` for MAQ `map` files produced by MAQ versions below 0.70 and `MAQMap` for more recent output. Use `fastq` for collections of fastq-format files. Quality assessment details vary depending on data source.

`qa,list-method`

  `dirPath` is a list of objects, all of the same class and typically derived from `ShortReadQ`, on which quality assessment is performed. All elements of the list must have names, and these should be unique.

### Value

An object derived from class `.QA`. Values contained in this object are meant for use by `report`

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

### See Also

`.QA`, `SolexaExportQA` `MAQMapQA` `FastqQA`

### Examples

    dirPath <- system.file(package="ShortRead", "extdata", "E-MTAB-1147")
    ## sample 1M reads / file
    qa <- qa(dirPath, "fastq.gz", BPPARAM=SerialParam())
    if (interactive())
        browseURL(report(qa))

    showMethods("qa", where=getNamespace("ShortRead"))

[Package ShortRead version 1.42.0 Index]