summarize_ggs_hubgenes {GeneTonic} | R Documentation

## Summarize information on the hub genes

### Description

Summarize information on the hub genes in the Gene-Geneset graph

### Usage

    summarize_ggs_hubgenes(g)

### Arguments

`g` | An `igraph` object, as generated by the `ggs_graph()` function

### Value

A data.frame object, formatted for use in `DT::datatable()`

### 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)

    ggs <- ggs_graph(
      res_enrich,
      res_de,
      anno_df
    )
    dt_df <- summarize_ggs_hubgenes(ggs)
    DT::datatable(dt_df, escape = FALSE)

[Package GeneTonic version 1.4.1 Index]