annotatedDMRs2Enrichr: Query different databases to find enriched proceses.

In GianlucaMattei/methyl.O: Annotate, Score and Visualize Differentially Methylated Regions

Query different databases to find enriched proceses.

Description

Query gene symbols from resulting annotations list in order to find enriched proceses.

Usage

annotatedDMRs2Enrichr(
  annotatedDMRs,
  active.features = c("promoters", "heads"),
  stat.filter = "P.value",
  stat.thr = 0.01,
  db = NULL
)

Arguments

annotatedDMRs	anotated DMRs list resulting from annotateDMRs() or scoreAnnotatedDMRs()
active.features	annotation level from the gene symbols are taken. Default = c('promoters', 'heads')
stat.filter	character indicating which type of statistics use for filtering results. Accepted values: 'P.value', 'Adjusted.P.value' or 'Overlap'. Default 'P.value'.
stat.thr	numeric value indicating the threshold to use for selcted statistical test. Default 0.01.
db	vector of characters indicating DBs to query. Default c("ClinVar_2019", "OMIM_Disease", "Elsevier_Pathway_Collection", "MSigDB_Hallmark_2020", "MSigDB_Oncogenic_Signatures", "GO_Biological_Process_2018", "Human_Phenotype_Ontology", "KEGG_2016", "NCI-Nature_2016", "Panther_2016", "Reactome_2016", "WikiPathways_2019_Human")

Value

data.frame with enriched processes

GianlucaMattei/methyl.O documentation built on Sept. 12, 2023, 11:53 p.m.