checkup_gtl {GeneTonic} | R Documentation

## Checking the `gtl` input object for GeneTonic

### Description

Checking the `gtl` ("GeneTonic list") input object for GeneTonic, with the correct content and format expected

### Usage

    checkup_gtl(gtl, verbose = FALSE)

### Arguments

`gtl` | A `DESeqDataSet` object, normally obtained after running your data through the `DESeq2` framework. This list should contain in the `dds` slot: A `DESeqDataSet` object in the `res_de`: A `DESeqResults` object in the `res_enrich`: A `data.frame` object, storing the result of the functional enrichment analysis in the `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 the `gtl` 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)

    gtl <- list(
      dds = dds_macrophage,
      res_de = res_de,
      res_enrich = res_enrich,
      annotation_obj = anno_df
    )

    checkup_gtl(gtl)
    # if all is fine, it should return an invisible NULL and a simple message

[Package GeneTonic version 1.6.4 Index]