DESeq2Report {regionReport} | R Documentation

## Generate a HTML/PDF report exploring DESeq2 results

### Description

This function generates a HTML report with exploratory data analysis plots for DESeq2 results created with DESeq. Other output formats are possible such as PDF but lose the interactivity. Users can easily append to the report by providing a R Markdown file to `customCode`, or can customize the entire template by providing an R Markdown file to `template`.

### Usage

    DESeq2Report(dds, project = "", intgroup, colors = NULL, res = NULL,
      nBest = 500, nBestFeatures = 20, customCode = NULL,
      outdir = "DESeq2Exploration", output = "DESeq2Exploration",
      browse = interactive(), device = "png", template = NULL,
      searchURL = "http://www.ncbi.nlm.nih.gov/gene/?term=", theme = NULL,
      digits = 2, ...)

### Arguments

`dds` | A DESeqDataSet object with the results from running DESeq.
`project` | The title of the project.
`intgroup` | interesting groups: a character vector of names in `colData(x)` to use for grouping. This parameter is passed to functions such as plotPCA.
`colors` | vector of colors used in heatmap. If `NULL`, then a a default set of colors will be used. This argument is passed to pheatmap.
`res` | A DESeqResults object. If `NULL`, then results will be used on `dds` with default parameters.
`nBest` | The number of features to include in the interactive table. Features are ordered by their adjusted p-values.
`nBestFeatures` | The number of best features to make plots of their counts. We recommend a small number, say 20.
`customCode` | An absolute path to a child R Markdown file with code to be evaluated before the reproducibility section. Its useful for users who want to customize the report by adding conclusions derived from the data and/or further quality checks and plots.
`outdir` | The name of output directory.
`output` | The name of output HTML file (without the html extension).
`browse` | If `TRUE` the HTML report is opened in your browser once it's completed.
`device` | The graphical device used when knitting. See more at http://yihui.name/knitr/options (`dev` argument).
`template` | Template file to use for the report. If not provided, will use the default file found in DESeq2Exploration/DESeq2Exploration.Rmd within the package source.
`searchURL` | A url used for searching the name of the features in the web. By default `http://www.ncbi.nlm.nih.gov/gene/?term=` is used which is the recommended option when features are genes. It's only used when the output is a HTML file.
`theme` | A ggplot2 theme to use for the plots made with ggplot2.
`digits` | The number of digits to round to in the interactive table of the top `nBestFeatures`. Note that p-values and adjusted p-values won't be rounded.
`...` | Arguments passed to other methods and/or advanced arguments. Advanced arguments: software The name of the package used for performing the differential expression analysis. Either `DESeq2` or `edgeR`. dge A DGEList object. `NULL` by default and only used by edgeReport. theCall The function call. `NULL` by default and only used by edgeReport. output_format Either `html_document`, `pdf_document` or `knitrBootstrap::bootstrap_document` unless you modify the YAML template. clean Logical, whether to clean the results or not. Passed to render.

### Details

Set `output_format` to `'knitrBootstrap::bootstrap_document'` or `'pdf_document'` if you want a HTML report styled by knitrBootstrap or a PDF report respectively. If using knitrBootstrap, we recommend the version available only via GitHub at https://github.com/jimhester/knitrBootstrap which has nicer features than the current version available via CRAN. You can also set the `output_format` to `'html_document'` for a HTML report styled by rmarkdown. The default is set to `'BiocStyle::html_document'`.

If you modify the YAML front matter of `template`, you can use other values for `output_format`.

The HTML report styled with knitrBootstrap can be smaller in size than the `'html_document'` report.

### Value

An HTML report with a basic exploration for the given set of DESeq2 results.

### Author(s)

Leonardo Collado-Torres

### Examples

    ## Load example data from the pasilla package
    library('pasilla')
    library('DESeq')
    library('DESeq2')

    ## Create DESeqDataSet object from the pasilla package
    data('pasillaGenes')
    countData <- counts(pasillaGenes)
    colData <- pData(pasillaGenes)[, c('condition', 'type')]
    dds <- DESeqDataSetFromMatrix(countData = countData,
       colData = colData,
       design = ~ condition)
    dds <- DESeq(dds)

    ## The output will be saved in the 'DESeq2Report-example' directory
    dir.create('DESeq2Report-example', showWarnings = FALSE, recursive = TRUE)

    ## Generate the HTML report
    report <- DESeq2Report(dds, 'DESeq2-example', c('condition', 'type'),
        outdir = 'DESeq2Report-example')

    if(interactive()) {
        ## Browse the report
        browseURL(report)
    }

    ## Not run:
    ## Note that you can run the example using:
    example('DESeq2Report', 'regionReport', ask=FALSE)

    ## End(Not run)

[Package regionReport version 1.20.1 Index]