mapIDs: Map moleculer identifiers using ENSEMBL BioMart

In vitkl/orthologsBioMART: Convenient functions for mapping orthologous genes using ENSEMBL BioMART

Description

mapIDs(): Map moleculer identifiers in a data.table using ENSEMBL BioMart - getBM

Usage

mapIDs(DT, ids2convert_col = "target", filters = "hgnc_symbol",
  map_to = "entrezgene", map_to_name = "target_entrezgene",
  biomart_dataset = "hsapiens_gene_ensembl")

Arguments

DT	data.table containing id to be converted
ids2convert_col	column in DT containing identifiers to be converted
filters	Filters (one, in ids2convert_col column) that should be used in the query. A possible list of filters can be retrieved using the function listFilters.
map_to	Attributes you want to retrieve. A possible list of attributes can be retrieved using the function listAttributes.
map_to_name	how to name the column in the output containing map_to identifiers
biomart_dataset	which BioMart dataset to use for mapping. Full list of possible options: listDatasets("ensembl")

Value

mapIDs(): data.table DT containing an additional column (map_to_name)

Examples

# load TF regulon data
combined_file = "../regulatory_networks_by_cmap/data/validation_TF_regulons/all_simp_regulons_w_pos_effect.tsv"
regulons = fread(combined_file, header = T, stringsAsFactors = F)
regulons = mapIDs(regulons)

vitkl/orthologsBioMART documentation built on Nov. 15, 2021, 9:20 p.m.