shake_enrichResult: Convert an enrichResult object

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

Convert an enrichResult object

Description

Convert an enrichResult object for straightforward use in GeneTonic()

Usage

shake_enrichResult(obj)

Arguments

obj	An enrichResult object, obtained via clusterProfiler (or also via reactomePA)

Details

This function is able to handle the output of clusterProfiler and reactomePA, as they both return an object of class enrichResult - 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_enrichrResult(), shake_fgseaResult(), shake_gprofilerResult(), shake_gsenrichResult(), 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")
res_de <- res_macrophage_IFNg_vs_naive
de_symbols_IFNg_vs_naive <- res_macrophage_IFNg_vs_naive[
  (!(is.na(res_macrophage_IFNg_vs_naive$padj))) &
    (res_macrophage_IFNg_vs_naive$padj <= 0.05), "SYMBOL"
]
bg_ids <- rowData(dds_macrophage)$SYMBOL[rowSums(counts(dds_macrophage)) > 0]
## Not run: 
library("clusterProfiler")
library("org.Hs.eg.db")
ego_IFNg_vs_naive <- enrichGO(
  gene = de_symbols_IFNg_vs_naive,
  universe = bg_ids,
  keyType = "SYMBOL",
  OrgDb = org.Hs.eg.db,
  ont = "BP",
  pAdjustMethod = "BH",
  pvalueCutoff = 0.01,
  qvalueCutoff = 0.05,
  readable = FALSE
)

res_enrich <- shake_enrichResult(ego_IFNg_vs_naive)
head(res_enrich)

## End(Not run)

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