annotate_cpg: Annotate the DMR resulting from epimutacions package

View source: R/annotate_cpg.R

annotate_cpgR Documentation

Annotate the DMR resulting from epimutacions package

Description

This function annotates a differentially methylated region

Usage

annotate_cpg(
  data,
  db,
  split = ",",
  epi_col = "cpg_ids",
  gene_col = "GencodeBasicV12_NAME",
  feat_col = "Regulatory_Feature_Group",
  relat_col = "Relation_to_Island",
  build = "37",
  omim = TRUE
)

Arguments

data

DataFrame-like object.

db

a character string specifying the Database to use for annotation. E.g: 'IlluminaHumanMethylationEPICanno.ilm10b2.hg19'.

split

a character string containing the separator for CpG ids. Default ','.

epi_col

CpG ids, should be row names in the data base.

gene_col

column name from where to extract gene names. Default: 'GencodeBasicV12_NAME'.

feat_col

column name from where to extract CpG feature groups. Default: 'Regulatory_Feature_Group'.

relat_col

column name from where to extract relation to island info. Default: 'Relation_to_Island'.

build

The build for bioMart. Default '37'.

omim

a boolean, if TRUE will annotate OMIMs as well. Takes a bit longer. Default TRUE.

Value

The function returns a DataFrame-like object annotated.


isglobal-brge/EpiMutations documentation built on April 20, 2024, 9:05 a.m.