R/getHGMDData.R

In gdelangel/genomicRTools: Genomic R Tools

#' getHGMDData
#'
#' Function to load from HGMD MySQL database. Assumes data schema as published by HGMD. Requires RMySQL package
#' @param geneName Gene name to load
#' @param user VEP transcript object or list. Needs to contain 'id', 'seq_region_name','start' and 'end' elements
#' @param password Return filtered-out sites (i.e. sites marked with anything other than PASS on vcf). Defaults to FALSE
#' @param host Max number of records to load. Set to -1 for no limit.
#' @param port Reference version. Defaults to "GRCh37".
#' @param dbname Reference version. Defaults to "GRCh37".
#' @keywords cats
#' @export
#' @examples
#' hgmddata<- getHGMDData('CFTR')

getHGMDData <- function(geneName,
                        user='hgmd',
                        password='hgmd',
                        host='192.168.99.100',
                        port='3306',
                        dbname='hgmd') {
  # load also HGMD
  con=dbConnect(MySQL(),username=user,password=password,host=host,unix.socket=port,dbname=dbname)

  # get all mutations
  res <- dbSendQuery(con,sprintf("select * from  \
                                mutnomen inner join allmut as h1 on h1.acc_num=mutnomen.acc_num  \
                               where gene='%s'",
                                 geneName))

  rawdat<-fetch(res,n=-1)
  #print(rawdat)
  #da <- subset(rawdat,
  #             select=-c(hgvsall,genename,dbsnp,fullname,allname,vol, page,year,new_date,reftag,author,chrom,comments,upstreamFLANK,downstreamFLANK))
  cleanHGVS <- paste0("c.",rawdat$hgvs[!is.na(rawdat$hgvs)])
  dbDisconnect(con)
  (list(hgvs=cleanHGVS,rawData=rawdat))

}