R/filterLowRepresentedCpGsinCohort.R

In isglobal-brge/EASIER: EwAS: quality control, meta-analysIs and EnRichment

#' Call Rate filter
#'
#' filters out all CpGs with missing call rates exceeding the provided value
#'
#' @param data dataframe with data to be filtered
#' @param colname string, column name that contains number of samples for each CpG
#' @param pcmissing numeric, máximum percent of missing samples allowed
#' @param Ntotal numeric, Number of samples in cohort
#'
#' @return filtered dataframe if colname exists
#'
#' @export
filterLowRepresentedCpGsinCohort <- function(data, colname, pcmissing, Ntotal, fileresume)
{

   if( !is.null(colname) & !is.null(pcmissing))
   {

      if( ! colname %in% names(data) ) {
         warning(paste0(colname, " does not exist in dataframe, no filter applied"))
         return(data)
      }

      if( pcmissing=='' | is.na(pcmissing) ){
         warning("No missing percentage defined, no filter applied")
         return(data)
      }

      totCpgs <- dim(data)[1]
      data$pecent <- data[,colname]/Ntotal
      data <- data[which(data$pecent>=pcmissing),]
      remCpGs <- totCpgs - dim(data)[1]

      # Report descriptive exclussions to a descriptive file
      if(!is.null(fileresume)) {
         write(sprintf('\n# %s', strrep("-",36)), file = fileresume, append = TRUE)
         write(sprintf('# Remove CpGs with low representation: '), file = fileresume, append = TRUE)
         write(sprintf('# %s\n', strrep("-",36)), file = fileresume, append = TRUE)
         write(sprintf('# Minimum percentage : %s\n', pcmissing), file = fileresume, append = TRUE)
         write(sprintf('# Total CpGs in data : %d', dim(data)[1]), file = fileresume, append = TRUE)
         write(sprintf('# Number of excluded CpGs: %d', remCpGs), file = fileresume, append = TRUE)
         write(sprintf('# Total CpGs after exclusion : %d\n', dim(data)[1] ), file = fileresume, append = TRUE)
         write(sprintf('# Percent excluded CpGs: %f %%\n', ((remCpGs/totCpgs)*100 )), file = fileresume, append = TRUE)
      }
   } else {
      if( is.null(colname)){
         warning("The column with number of samples for CpG was not defined, no filter applied")
      } else {
         warning("The missing percentage was not defined, no filter applied")
      }
   }

   return(data)

}