BiomartSearch

Example of a search with str_detect

Can use grepl or %in% or other tools depending

on what terms you are searching for

#read in possible search terms
library(tidyverse)

## Warning: package 'ggplot2' was built under R version 4.4.3

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library(biomaRt)
data <- read.csv('phenotype_options.csv',header=FALSE)

#define vector of possible terms
result1<-data[str_detect(data$V1, "10-heptadecenoate"), ]

#Select mart
ensembl=useMart("ENSEMBL_MART_SNP",
                dataset="hsapiens_snp")

#Select attributes (choose at least 6 related to your search)
att1 <- c('refsnp_id',
          'minor_allele',
          'minor_allele_freq',
          'phenotype_name',
          'phenotype_description',
          'clinical_significance',
          'associated_variant_risk_allele',
          'p_value',
          'validated')

#Run search
searchResults <-getBM(att1,
                      filters= 'phenotype_description',
                      values= result1, 
                      mart=ensembl)

#Write results to file
write.csv(searchResults,'search.csv',row.names=FALSE)