Description Usage Arguments Value Note
retrieve human gene info from ensembl
1 2 3 4 5 6 7 | mart.geneinfo(
values = c("COMT", "CRHR1"),
filters = "hgnc_symbol",
attributes = c("ensembl_gene_id", "hgnc_symbol", "description", "chromosome_name",
"start_position", "end_position"),
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, the kind/type of your input data, 'hgnc_symbol', "ensembl_gene_id"
|
attributes |
column attributes, what to return |
host |
default 'www.ensembl.org'. Other eg, 'grch37.ensembl.org', 'aug2017.archive.ensembl.org'. See all, run |
returns a data frame
In case multple filters are in use, the values argument requires a list of values where each position in the list corresponds to the position of the filters in the filters argument. eg,
filters=c("chr_name","start","end")
values=list(8,148350, 158612)
for multiple regions, use:
filters="chromosomal_region"
values=c('17:43750137:43750137','17:43750172:43750172')
values=list(chr_name=17,start=c(43750137,43750172),end=c(43750137,43750172))
should retrieve 43750137:43750137, 43750172:43750172
but it seems to run for 43750137:43750172, which is not desired
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