checkup_GeneTonic {GeneTonic} | R Documentation

## Checking the input objects for GeneTonic

### Description

Checking the input objects for GeneTonic, whether these are all set for running the app

### Usage

    checkup_GeneTonic(dds, res_de, res_enrich, annotation_obj, verbose = FALSE)

### 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. See more in the main function, `GeneTonic()`, to check the formatting requirements (a minimal set of columns should be present).
`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.
`verbose` | Logical, to control level of verbosity of the messages generated

### Details

Some suggestions on the requirements for each parameter are returned in the error messages.

### Value

Invisible NULL

### 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)

    checkup_GeneTonic(
      dds = dds_macrophage,
      res_de = res_de,
      res_enrich = res_enrich,
      annotation_obj = anno_df
    )
    # if all is fine, it should return an invisible NULL and a simple message

[Package GeneTonic version 1.6.4 Index]