mart.snpinfo: retrieve human snp info from ensembl

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

Description

retrieve human snp info from ensembl

Usage

mart.snpinfo(
  values = c("rs2075507", "rs547420070", "rs77274555"),
  filters = "snp_filter",
  attributes = c("refsnp_id", "validated", "allele", "allele_1", "minor_allele",
    "minor_allele_freq", "clinical_significance", "chr_name", "chrom_start", "chrom_end",
    "ensembl_gene_stable_id"),
  host = NULL
)

mart.snpinfo2(
  values = "rs2097603",
  filters = "snp_synonym_filter",
  attributes = c("refsnp_id", "chr_name", "chrom_start", "chrom_end", "allele",
    "allele_1", "minor_allele", "minor_allele_freq", "ensembl_gene_stable_id"),
  host = NULL
)

Arguments

values	the actual input data values, cannot be all empty, but partial empty/NA fine, rs number, eg, 'rs2075507', c('rs2075507', 'rs547420070', 'rs77274555'); to search archived synonymous rs number, use mart.snpinfo2
filters	row filters in the db, the kind/type of your input data
attributes	column attributes, what to return, eg, 'synonym_name'
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.