edgeReport {regionReport} | R Documentation

## Generate a HTML/PDF report exploring edgeR results

### Description

This function generates a HTML report with exploratory data analysis plots for edgeR results created. Other output formats are possible such as PDF reports but they 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

    edgeReport(dge, object, project = "", intgroup, colors = NULL,
      pAdjustMethod = "BH", alpha = 0.1, independentFiltering = FALSE,
      filter, theta, filterFun, nBest = 500, nBestFeatures = 20,
      customCode = NULL, outdir = "edgeRexploration",
      output = "edgeRexploration", browse = interactive(),
      device = "png", template = NULL,
      searchURL = "http://www.ncbi.nlm.nih.gov/gene/?term=", theme = NULL,
      digits = 2, ...)

### Arguments

`dge` | A DGEList object.
`object` | A DGEExact or DGELRT object that contains p-values stored in `object$table$PValue`.
`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.
`pAdjustMethod` | the method to use for adjusting p-values, see p.adjust. This argument will be passed to results.
`alpha` | the significance cutoff used for optimizing the independent filtering (by default 0.1). If the adjusted p-value cutoff (FDR) will be a value other than 0.1, alpha should be set to that value. This argument will be passed to results.
`independentFiltering` | logical, whether independent filtering should be applied automatically. By default it's set to `FALSE` in contrast with the default used in results to match `edgeR`'s behavior.
`filter` | the vector of filter statistics over which the independent filtering will be optimized. By default the logCPM will be used if `independentFiltering` is set to `TRUE`. It can also be a length 1 character vector specifying one of the column names of `object$table`.
`theta` | the quantiles at which to assess the number of rejections from independent filtering. This argument is passed results.
`filterFun` | an optional custom function as described in results.
`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.

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

This report is similar to the one created by DESeq2Report with two additional plots exclusive for edgeR results. We designed the reports to be very similar intentionally and use the Bioconductor package DEFormats to achieve this goal.

### Value

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

### Author(s)

Leonardo Collado-Torres

### Examples

    ## Create example data using DEFormats
    library('DEFormats')
    set.seed(20160407)
    counts <- simulateRnaSeqData()
    group <- rep(c("A", "B"), each = 3)

    ## Create DGEList object
    library('edgeR')
    dge <- DGEList(counts, group = group)

    ## Perform DE analysis with edgeR
    design <- model.matrix( ~ group)
    dge <- estimateDisp(dge, design)
    fit <- glmFit(dge, design)
    lrt <- glmLRT(fit, coef = 2)

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

    ## Generate the HTML report
    report <- edgeReport(dge, lrt, project = 'edgeR-example', intgroup = 'group',
        outdir = 'edgeReport-example')

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

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

    ## End(Not run)

[Package regionReport version 1.21.1 Index]