humarray (version 1.2)

get.immunobase.snps: Download GWAS hits from t1dbase.org

Description

Deprecated as this data is no longer available online Retrieve human disease top GWAS hits from t1dbase in build hg19 coords (37). 28 Diseases currently available

Usage

get.immunobase.snps(disease = "T1D", snps.only = TRUE, show.codes = FALSE)

Arguments

disease

integer (1-28), or character (abbreviation), or full name of one of the listed diseases. A full list of options can be obtained by setting show.codes=TRUE.

snps.only

logical, default is just to return a list of rs-ids. Setting FALSE gives a table

show.codes

logical, if set to TRUE, instead of looking up t1dbase, will simply return a table of available diseases with their index numbers and abbreviations.

Value

A character vector of SNP rs-ids

References

PMID: 20937630

Examples

# NOT RUN {
get.immunobase.snps(show.codes=TRUE) # show codes/diseases available to download
# }
# NOT RUN {
# Deprecated as this data is no longer available online
# get.immunobase.snps(disease="CEL") # get SNP ids for celiac disease
# get.immunobase.snps(disease="AS") # get SNP ids for Ankylosing Spondylitis in build-37/hg19
# get.immunobase.snps(disease=27) # get SNP ids for Alopecia Areata
# get.immunobase.snps("Vitiligo")
# }