R: Summarize quality assessment results into a report

report {ShortRead}

R Documentation

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")

Arguments

`x`	An object returned by `qa`, usually derived from class `.QA`
`...`	Additional arguments used by specific methods. See specific methods for details.
`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

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")

[Package ShortRead version 1.2.1 Index]