R/probe_features_get.R

In drake69/semseeker: Stochastic Epigenetic Mutations SEM Seeker

probe_features_get <- function(area_subarea)
{
  ssEnv <- get_session_info()

  if(is.null(ssEnv$tech) | ssEnv$tech=="")
    stop("ERROR: ", Sys.time(), " Probes get should be called once defined which tech is used.")

  probe_features <- semseeker::pp_tot
  probe_features <- probe_features[ probe_features[,ssEnv$tech], ]
  probe_features$END <- probe_features$START

  if( grepl("CHR", area_subarea)  || grepl("PROBE",area_subarea))
    probe_features <- unique(stats::na.omit(probe_features[ c(ssEnv$tech,"PROBE","CHR","START","END")]))
  else
    probe_features <- unique(stats::na.omit(probe_features[ c(ssEnv$tech,"PROBE","CHR","START","END",area_subarea)]))

  # needed to avoid special elaboration in other function on chromosome or probe
  if( grepl("CHR", area_subarea))
    probe_features$CHR_WHOLE <- paste("chr",probe_features$CHR, sep="")

  if(grepl("PROBE",area_subarea))
      probe_features$PROBE_WHOLE <- probe_features$PROBE

  probe_features <- probe_features[ ,-c(which(colnames(probe_features) %in% ssEnv$tech )) ]
  return(probe_features)
}