GeneTonic {GeneTonic} | R Documentation

## GeneTonic

### Description

GeneTonic, main function for the Shiny app

### Usage

    GeneTonic(dds, res_de, res_enrich, annotation_obj, gtl = NULL, project_id = "")

### Arguments

`dds` | A `DESeqDataSet` object, normally obtained after running your data through the `DESeq2` framework.
`res_de` | A `DESeqResults` object. As for the `dds` parameter, this is also commonly used in the `DESeq2` framework.
`res_enrich` | A `data.frame` object, storing the result of the functional enrichment analysis. Required columns for enjoying the full functionality of `GeneTonic()` include: a gene set identifier (e.g. GeneOntology id, `gs_id`) and its term description (`gs_description`) a numeric value for the significance of the enrichment (`gs_pvalue`) a column named `gs_genes` containing a comma separated vector of the gene names associated to the term, one for each term the number of genes in the geneset of interest detected as differentially expressed (`gs_de_count`), or in the background set of genes (`gs_bg_count`) See `shake_topGOtableResult()` or `shake_enrichResult()` for examples of such formatting helpers
`annotation_obj` | A `data.frame` object, containing two columns, `gene_id` with a set of unambiguous identifiers (e.g. ENSEMBL ids) and `gene_name`, containing e.g. HGNC-based gene symbols. This object can be constructed via the `org.eg.XX.db` packages, e.g. with convenience functions such as `pcaExplorer::get_annotation_orgdb()`.
`gtl` | A `GeneTonic`-list object, containing in its slots the arguments specified above: `dds`, `res_de`, `res_enrich`, and `annotation_obj` - the names of the list must be specified following the content they are expecting
`project_id` | A character string, which can be considered as an identifier for the set/session, and will be e.g. used in the title of the report created via `happy_hour()`

### Value

A Shiny app object is returned, for interactive data exploration

### Author(s)

Federico Marini

### Examples

    library("macrophage")
    library("DESeq2")
    library("org.Hs.eg.db")
    library("AnnotationDbi")

    # dds object
    data("gse", package = "macrophage")
    dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition)
    rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
    dds_macrophage <- estimateSizeFactors(dds_macrophage)

    # annotation object
    anno_df <- data.frame(
      gene_id = rownames(dds_macrophage),
      gene_name = mapIds(org.Hs.eg.db,
        keys = rownames(dds_macrophage),
        column = "SYMBOL",
        keytype = "ENSEMBL"
      ),
      stringsAsFactors = FALSE,
      row.names = rownames(dds_macrophage)
    )

    # res object
    data(res_de_macrophage, package = "GeneTonic")
    res_de <- res_macrophage_IFNg_vs_naive

    # res_enrich object
    data(res_enrich_macrophage, package = "GeneTonic")
    res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive)
    res_enrich <- get_aggrscores(res_enrich, res_de, anno_df)

    # now everything is in place to launch the app
    if (interactive()) {
      GeneTonic(
        dds = dds_macrophage,
        res_de = res_de,
        res_enrich = res_enrich,
        annotation_obj = anno_df,
        project_id = "myexample"
      )
    }
    # alternatively...
    gtl_macrophage <- GeneTonic_list(
      dds = dds_macrophage,
      res_de = res_de,
      res_enrich = res_enrich,
      annotation_obj = anno_df
    )
    # GeneTonic(gtl = gtl_macrophage)

[Package GeneTonic version 1.4.1 Index]