Convert an enrichResult object for straightforward use in GeneTonic()

shake_enrichResult(obj)

Arguments

obj

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

Value

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

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.

See also

Examples

# dds
library("macrophage")
library("DESeq2")
data(gse)
dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition)
#> using counts and average transcript lengths from tximeta
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]
if (FALSE) {
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)
}