mart.geneconv: convert from gene name to id, id to name, id to id

Description Usage Arguments Value Note

View source: R/biomart.R

Description

convert from gene name to id, id to name, id to id

Usage

1
2
3
mart.geneconv(values = c("ENSG00000118473", "ENSG00000162426"),
  filters = "ensembl_gene_id", attributes = c("ensembl_gene_id",
  "hgnc_symbol", "hgnc_id", "entrezgene"), host = NULL)

Arguments

values

the actual input data values, cannot be all empty, but partial empty/NA fine, ensembl_gene_id, ENSG00000118473, c('ENSG00000118473', 'ENSG00000162426'). If vector, should be the same id type

filters

row filters in the db, from what id, 'hgnc_symbol'
"ensembl_gene_id"(ENSG00000118473),"hgnc_id"(HGNC:25412),"entrezgene" (84251),"kegg_enzyme"(00010+1.1.1.1),"go_id"(GO:0030122),"ucsc"(uc057hhx.1)

attributes

column attributes, to what id(s), external max 3

host

default 'www.ensembl.org'. Other eg, 'grch37.ensembl.org', 'aug2017.archive.ensembl.org'. See all, run mart.list

Value

returns a data frame

Note

To allow BioMart to return results in a reasonable amound of time, Ensembl has restricted the number of External references that you can select to 3. ensembl_gene_id–>ensembl_gene_id still works, but if the id does not exist, returns empty data frame


jerryzhujian9/bzR documentation built on May 16, 2019, 7:13 p.m.