shake_enrichResult {GeneTonic} | R Documentation |
Convert an enrichResult object for straightforward use in GeneTonic()
shake_enrichResult(obj)
obj |
An |
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.
A data.frame
compatible for use in GeneTonic()
as res_enrich
Other shakers:
shake_davidResult()
,
shake_enrichrResult()
,
shake_fgseaResult()
,
shake_gprofilerResult()
,
shake_topGOtableResult()
# 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)