R/makeBPQuery.R

In yyolanda/toolKitty:

#' Query variants with chromosome and position
#'
#' This function allows you to query SNP information given its chromosome and position.
#' @param chrom What's the chromosome number of the SNP?
#' @param pos What's the position of the SNP on the chromosome?
#' @param fields What would you like to know about the SNP?
#' @keywords SNP query
#' @export
#' @examples
#' makeBPQuery(4, 12345679, c("cadd.consequence", "dbsnp.gene"))


makeBPQuery = function(chrom, pos, fields){
  queryResult = list()

  for(i in 1:length(chrom)){
    q = paste0('cadd.chrom:', chrom[i], ' AND cadd.pos:', pos[i])
    result = queryVariant(q=q, fields=fields)$hits

    if (!length(result) == 0){
      result = list(result)
      queryResult = c(queryResult, result)
    }
  }
  return(queryResult)
}