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")
    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

    showMethods("report")

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

[Package ShortRead version 1.42.0 Index]