ShortRead: report – R documentation

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report

Summarize quality assessment results into a report

Description

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

Usage

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>

Examples

showMethods("report")

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

ShortRead

FASTQ input and manipulation

v1.48.0

Artistic-2.0

Authors

Martin Morgan, Michael Lawrence, Simon Anders

Initial release