qa2 {ShortRead} | R Documentation

## (Updated) quality assessment reports on short reads

### Description

This page summarizes an updated approach to quality assessment reports in `ShortRead`.

### Usage

    ## Input source for short reads
    QAFastqSource(con = character(), n = 1e+06, readerBlockSize = 1e+08,
        flagNSequencesRange = NA_integer_, ...,
        html = system.file("template", "QASources.html", package="ShortRead"))
    QAData(seq = ShortReadQ(), filter = logical(length(seq)), ...)

    ## Possible QA elements
    QAFrequentSequence(useFilter = TRUE, addFilter = TRUE,
        n = NA_integer_, a = NA_integer_, flagK=.8, reportSequences = FALSE,
        ...)
    QANucleotideByCycle(useFilter = TRUE, addFilter = TRUE, ...)
    QANucleotideUse(useFilter = TRUE, addFilter = TRUE, ...)
    QAQualityByCycle(useFilter = TRUE, addFilter = TRUE, ...)
    QAQualityUse(useFilter = TRUE, addFilter = TRUE, ...)
    QAReadQuality(useFilter = TRUE, addFilter = TRUE,
        flagK = 0.2, flagA = 30L, ...)
    QASequenceUse(useFilter = TRUE, addFilter = TRUE, ...)
    QAAdapterContamination(useFilter = TRUE, addFilter = TRUE,
        Lpattern = NA_character_, Rpattern = NA_character_,
        max.Lmismatch = 0.1, max.Rmismatch = 0.2, min.trim = 9L, ...)

    ## Order QA report elements
    QACollate(src, ...)

    ## perform analysis
    qa2(object, state, ..., verbose=FALSE)

    ## Outputs from qa2
    QA(src, filtered, flagged, ...)
    QAFiltered(useFilter = TRUE, addFilter = TRUE, ...)
    QAFlagged(useFilter = TRUE, addFilter = TRUE, ...)

    ## Summarize results as html report
    ## S4 method for signature 'QA'
    report(x, ..., dest = tempfile(), type = "html")

    ## additional methods; 'flag' is not fully implemented
    flag(object, ..., verbose=FALSE)

    ## S4 method for signature 'QASummary'
    rbind(..., deparse.level = 1)

### Arguments

`con` | `character(1)` file location of fastq input, as used by `FastqSampler`.
`n` | `integer(1)` number of records to input, as used by `FastqStreamer` (`QAFastqSource`). `integer(1)` number of sequences to tag as ‘frequent’ (`QAFrequentSequence`).
`readerBlockSize` | integer(1) number of bytes to input, as used by `FastqStreamer`.
`flagNSequencesRange` | `integer(2)` minimum and maximum reads above which source files will be flagged as outliers.
`html` | `character(1)` location of the HTML template for summarizing this report element.
`seq` | `ShortReadQ` representation of fastq data.
`filter` | `logical()` vector with length equal to `seq`, indicating whether elements of `seq` are filtered (`TRUE`) or not.
`useFilter, addFilter` | `logical(1)` indicating whether the QA element should be calculating using the filtered (`useFilter=TRUE`) or all reads, and whether reads failing the QA element should be added to the filter used by subsequent steps (`addFilter = TRUE`) or not.
`a` | `integer(1)` count of number of sequences above which a read will be considered ‘frequent’ (`QAFrequentSequence`).
`flagK, flagA` | `flagK` `numeric(1)` between 0 and 1 indicating the fraction of frequent sequences greater than or equal to `n` or `a` above which a fastq file will be flagged (`QAFrequentSequence`). `flagK` `numeric{1}` between 0 and 1 and `flagA` `integer(1)` indicating that a run should be flagged when the fraction of reads with quality greater than or equal to `flagA` falls below threshold `flagK`.
`reportSequences` | `logical(1)` indicating whether frequent sequences are to be reported.
`Lpattern, Rpattern, max.Lmismatch, max.Rmismatch, min.trim` | Parameters influencing adapter identification, see `matchPattern`.
`src` | The source, e.g., `QAFastqSource`, on which the quality assessment report will be based.
`object` | An instance of class derived from `QA` on which quality metrics will be derived; for end users, this is usually the result of `QACollate`.

.

`state` | The data on which quality assessment will be performed; this is not usually necessary for end-users.
`verbose` | `logical(1)` indicating whether progress reports should be reported.
`filtered, flagged` | Primarily for internal use, instances of `QAFiltered` and `QAFlagged`.
`x` | An instance of `QA` on which a report is to be generated.
`dest` | `character(1)` providing the directory in which the report is to be generated.
`type` | `character(1)` indicating the type of report to be generated; only “html” is supported.
`deparse.level` | see `rbind`.
`...` | Additional arguments, e.g., `html` to specify the location of the html source to use as a template for the report.

### Details

Use `QACollate` to specify an order in which components of a QA report are to be assembled. The first argument is the data source (e.g., `QAFastqSource`).

Functions related to data input include:

`QAFastqSource`

  defines the location of fastq files to be included in the report. `con` is used to construct a `FastqSampler` instance, and records are processed using `qa2,QAFastqSource-method`.

`QAData`

  is a class for representing the data during the QA report generation pass; it is primarily for internal use.

Possible elements in a QA report are:

`QAFrequentSequence`

  identifies the most-commonly occuring sequences. One of `n` or `a` can be non-NA, and determine the number of frequent sequences reported. `n` specifies the number of most-frequent sequences to filter, e.g., `n=10` would filter the top 10 most commonly occurring sequences; `a` provides a threshold frequency (count) above which reads are filtered. The sample is flagged when a fraction `flagK` of the reads are filtered.

  `reportSequences` determines whether the most commonly occuring sequences, as determined by `n` or `a`, are printed in the html report.

`QANucleotideByCycle`

  reports nucleotide frequency as a function of cycle.

`QAQualityByCycle`

  reports average quality score as a function of cycle.

`QAQualityUse`

  summarizes overall nucleotide qualities.

`QAReadQuality`

  summarizes the distribution of read qualities.

`QASequenceUse`

  summarizes the cumulative distribution of reads occurring 1, 2, ... times.

`QAAdapterContamination`

  reports the occurrence of ‘adapter’ sequences on the left and / or right end of each read.

### 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`.

### Examples

    dirPath <- system.file(package="ShortRead", "extdata", "E-MTAB-1147")
    fls <- dir(dirPath, "fastq.gz", full=TRUE)

    coll <- QACollate(QAFastqSource(fls), QAReadQuality(),
        QAAdapterContamination(), QANucleotideUse(),
        QAQualityUse(), QASequenceUse(),
        QAFrequentSequence(n=10), QANucleotideByCycle(),
        QAQualityByCycle())
    x <- qa2(coll, BPPARAM=SerialParam(), verbose=TRUE)

    res <- report(x)
    if (interactive())
        browseURL(res)

[Package ShortRead version 1.42.0 Index]