shake_gsenrichResult {GeneTonic} | R Documentation

## Convert a gseaResult object

### Description

Convert a gseaResult object for straightforward use in `GeneTonic()`

### Usage

    shake_gsenrichResult(obj)

### Arguments

`obj` | A `gseaResult` object, obtained via `clusterProfiler`

### Details

This function is able to handle the output of `clusterProfiler`'s `gseGO` and `GSEA`, as they both return an object of class `gseaResult` - and this in turn contains the information required to create correctly a `res_enrich` object.

### Value

A `data.frame` compatible for use in `GeneTonic()` as `res_enrich`

### See Also

Other shakers: `shake_davidResult()`, `shake_enrichResult()`, `shake_enrichrResult()`, `shake_fgseaResult()`, `shake_gprofilerResult()`, `shake_topGOtableResult()`

### Examples

    # dds
    library("macrophage")
    library("DESeq2")
    data(gse)
    dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition)
    rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)

    # res object
    data(res_de_macrophage, package = "GeneTonic")
    sorted_genes <- sort(
      setNames(res_macrophage_IFNg_vs_naive$log2FoldChange,
               res_macrophage_IFNg_vs_naive$SYMBOL),
      decreasing = TRUE
    )
    ## Not run:
    library("clusterProfiler")
    library("org.Hs.eg.db")
    gsego_IFNg_vs_naive <- gseGO(
      geneList = sorted_genes,
      ont = "BP",
      OrgDb = org.Hs.eg.db,
      keyType = "SYMBOL",
      minGSSize = 10,
      maxGSSize = 500,
      pvalueCutoff = 0.05,
      verbose = TRUE
    )

    res_enrich <- shake_gsenrichResult(gsego_IFNg_vs_naive)
    head(res_enrich)
    gtl_macrophage <- GeneTonic_list(
      dds = dds_macrophage,
      res_de = res_macrophage_IFNg_vs_naive,
      res_enrich = res_enrich,
      annotation_obj = anno_df
    )

    ## End(Not run)

[Package GeneTonic version 1.6.4 Index]