KO_enrich | R Documentation |
This function performs KO enrichment analysis using the 'clusterProfiler' package.
KO_enrich(
ko_stat,
padj_threshold = 0.05,
logFC_threshold = NULL,
add_mini = NULL,
p.adjust.method = "BH",
type = c("pathway", "module")[1],
feature = "ko",
modulelist = NULL,
verbose = TRUE
)
as.enrich_res(gsea_res)
ko_stat |
ko_stat dataframe from |
padj_threshold |
p.adjust threshold to determine whether a feature significant or not. p.adjust < padj_threshold, default: 0.05 |
logFC_threshold |
logFC threshold to determine whether a feature significant or not. abs(logFC)>logFC_threshold, default: NULL |
add_mini |
add_mini when calculate the logFC. e.g (10+0.1)/(0+0.1), default 0.05*min(avg_abundance) |
p.adjust.method |
The method used for p-value adjustment (default: "BH"). |
type |
"pathway" or "module" for default KOlist_file. |
feature |
one of "ko", "gene", "compound" |
modulelist |
NULL or customized modulelist dataframe, must contain "id","K_num","KOs","Description" columns. Take the 'KOlist' as example, use |
verbose |
logical |
gsea_res |
gsea_res from KO_gsea |
A data frame containing the enrichment results.
enrich_res object
Other common_enrich:
KO_fisher()
,
KO_gsa()
,
KO_gsea()
,
KO_gsva()
,
KO_padog()
,
KO_safe()
,
KO_sea()
,
plot_enrich_res()
## use `enricher` from the `clusterProfiler` package.
if (requireNamespace("clusterProfiler")) {
data("reporter_score_res")
enrich_res <- KO_enrich(reporter_score_res)
plot(enrich_res)
}
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