report: Summarize quality assessment results into a report

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

Description

This generic function summarizes results from evaluation of qa into a report. Available report formats vary depending on the data analysed.

Usage

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report(x, ..., dest=tempfile(), type="html")
report_html(x, dest, type, ...)

Arguments

x

An object returned by qa, usually derived from class .QA

...

Additional arguments used by specific methods.

All methods with type="html" support the argument cssFile, which is a named, length 1 character vector. The value is a path to a CSS file to be incorporated into the report (e.g., system.file("template", "QA.css", package="ShortRead")). The name of cssFile is the name of the CSS file as seen by the html report (e.g., “QA.css”).

See specific methods for details on additional ... arguments.

dest

The output destination for the final report. For type="html" this is a directory; for (deprecated) type="pdf" this is a file.

type

A text string defining the type of report; available report types depend on the type of object x; usually this is “html”.

Details

report_html is meant for use by package authors wishing to add methods for creating HTML reports; users should always invoke report.

The following methods are defined:

x="BowtieQA", ..., dest=tempfile(), type="html"

Produce an HTML-based report from an object of class BowtieQA.

x="FastqQA", ..., dest=tempfile(), type="html"

Produce an HTML-based report from an object of class FastqQA.

x="MAQMapQA", ..., dest=tempfile(), type="html"

Produce an HTML-based report from an object of class MAQMapQA.

x="SolexaExportQA", ..., dest=tempfile(), type="html"

Produce an HTML-based report from an object of class SolexaExportQA.

x="SolexaExportQA", ..., dest=tempfile(), type="pdf"

(Deprecated) Produce an PDF report from an object of class SolexaExportQA.

x="SolexaPath", ..., dest=tempfile(), type="html"

Produce an HTML report by first visiting all _export.txt files in the analysisPath directory of x to create a SolexaExportQA instance.

x="SolexaPath", ..., dest=tempfile(), type="pdf"

(Deprecated) Produce an PDF report by first visiting all _export.txt files in the analysisPath directory of x to create a SolexaExportQA instance.

x="ANY", ..., dest=tempfile(), type="ANY"

This method is used internally

Value

This function is invoked for its side effect; the return value is the name of the directory or file where the report was created.

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

See Also

SolexaExportQA

Examples

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showMethods("report")

## default CSS file
cssFile <- c(QA.css=system.file("template", "QA.css",
                                package="ShortRead"))
noquote(readLines(cssFile))


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