Description Usage Arguments Value Note
convert from gene name to id, id to name, id to id
1 2 3 4 5 6 | mart.geneconv(
values = c("ENSG00000118473", "ENSG00000162426"),
filters = "ensembl_gene_id",
attributes = c("ensembl_gene_id", "hgnc_symbol", "hgnc_id", "entrezgene"),
host = NULL
)
|
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'
|
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 |
returns a data frame
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
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