qa2: (Updated) quality assessment reports on short reads
In ShortRead: FASTQ input and manipulation

Description Usage Arguments Details Value Author(s) See Also Examples

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

## 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)

`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.

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.

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

Martin Morgan <mtmorgan@fhcrc.org>

QA.

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)