Phenotype-Based Biomart Search

library(biomaRt)
ensembl=useMart("ENSEMBL_MART_SNP",
                dataset="hsapiens_snp")
#Make a vector for your filters
filter1 <- 'phenotype_description'

#Make a vector for the values that will go into your filter
#Change this for the assignment to be the list of 100 
#rsids from last week
values1 <- c('Arsenic metabolism','Hypermanganesemia with dystonia polycythemia and cirrhosis','Lead levels in blood')

#List attributes, click on myAttributes in Environment to view options
myAttributes <- listAttributes(ensembl)

#Make a variable for your attributes
#Look through list to find columns that could be useful in filtering
#or writing up your report
att1 <- c('refsnp_id','minor_allele','minor_allele_freq','phenotype_name',
          'phenotype_description','clinical_significance',
          'associated_variant_risk_allele','p_value','validated')

searchResults <-getBM(att1,
                      filters= filter1,
                      values= values1, mart=ensembl)