functionEnrich: The functionEnrich function

In gevaertlab/EpiMix: EpiMix: an integrative tool for the population-level analysis of DNA methylation

The functionEnrich function

Description

Perform functional enrichment analysis for the differentially methylated genes occurring in the significant CpG-gene pairs.

Usage

functionEnrich(
  EpiMixResults,
  methylation.state = "all",
  enrich.method = "GO",
  ont = "BP",
  simplify = TRUE,
  cutoff = 0.7,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  qvalueCutoff = 0.2,
  save.dir = "."
)

Arguments

EpiMixResults	List of the result objects returned from the EpiMix function.
methylation.state	character string indicating whether to use all the differentially methylated genes or only use the hypo- or hyper-methylated genes for enrichment analysis. Can be either 'all', 'Hyper' or 'Hypo'.
enrich.method	character string indicating the method to perform enrichment analysis, can be either 'GO' or 'KEGG'.
ont	character string indicating the aspect for GO analysis. Can be one of 'BP' (i.e., biological process), 'MF' (i.e., molecular function), and 'CC' (i.e., cellular component) subontologies, or 'ALL' for all three.
simplify	boolean value indicating whether to remove redundancy of enriched GO terms.
cutoff	if simplify is TRUE, this is the threshold for similarity cutoff of the ajusted p value.
pvalueCutoff	adjusted pvalue cutoff on enrichment tests to report
pAdjustMethod	one of 'holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none'
qvalueCutoff	qvalue cutoff on enrichment tests to report as significant. Tests must pass i) pvalueCutoff on unadjusted pvalues, ii) pvalueCutoff on adjusted pvalues and iii) qvalueCutoff on qvalues to be reported.
save.dir	path to save the enrichment table.

Value

a clusterProfiler enrichResult instance

Examples

library(clusterProfiler)
library(org.Hs.eg.db)

data(Sample_EpiMixResults_Regular)

enrich.results <- function.enrich(
 EpiMixResults = Sample_EpiMixResults_Regular,
 enrich.method = 'GO',
 ont = 'BP',
 simplify = TRUE,
 save.dir = ''
)

gevaertlab/EpiMix documentation built on July 20, 2023, 9:28 a.m.