shake_gsenrichResult: Convert a gseaResult object

In federicomarini/GeneTonic: Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

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 <- GeneTonicList(
  dds = dds_macrophage,
  res_de = res_macrophage_IFNg_vs_naive,
  res_enrich = res_enrich,
  annotation_obj = anno_df
)

## End(Not run)

federicomarini/GeneTonic documentation built on Oct. 10, 2024, 8:49 p.m.