R/returnVariantDatatable.R

In SNPannotator: Investigating the Functional Characteristics of Selected SNPs and Their Vicinity Genomic Region

returnVariantDatatable <- function(varNum , varInfo, database )
{

  # create an empty data table where the first row is the target SNP
  tab <-  getVariantData(varNum,varInfo,varInfo,database, LD = 1)

  # fill the above data table if any variant found in high LD
  if(!is.null(varInfo$LDList) & !is.null(ncol(varInfo$LDList)))
  {
    LDTable <- setDT(varInfo$LDList)

    for(i in seq_len(length(varInfo$LDlistFull)))
    {
      if(!is.null(varInfo$LDlistFull[[i]]$name) & length(varInfo$LDlistFull[[i]]$population) > 0)
      {
        LD = LDTable[variation2 == varInfo$LDlistFull[[i]]$name, r2]
        tab <- rbind(tab, getVariantData(varNum,varInfo,varInfo$LDlistFull[[i]],database,LD))
      }
    }
  }

  tab <- tab[order(-LD),]

  return(tab)
}