mart.geneinfo: retrieve human gene info from ensembl

In jerryzhujian9/bz: bio Zhu's miscellaneous R functions

Description

retrieve human gene info from ensembl

Usage

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/bz documentation built on Jan. 12, 2022, 9:45 a.m.