mart.geneinfo: retrieve human gene info from ensembl

Description Usage Arguments Value Note

View source: R/biomart.R

Description

retrieve human gene info from ensembl

Usage

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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)

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, the kind/type of your input data, 'hgnc_symbol', "ensembl_gene_id"
"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, what to return

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

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


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