annotate_cpg: Annotate the DMR resulting from epimutacions package

In isglobal-brge/epimutacions: Robust outlier identification for DNA methylation data

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/epimutacions documentation built on April 22, 2024, 4:08 a.m.