R/replace_outliers.R

In kuppal2/xmsPANDA: R Package for Biomarker Discovery, Network, and Data Exploratory Analysis

replace_outliers <-
function(cdata,replace.by.NA=FALSE,iqr.multiplier=1.5){
  data_sum<-summary(cdata,na.rm=TRUE)
  iqr_value<-data_sum[5]-data_sum[2]
  upper_limit<-data_sum[5]+iqr.multiplier*iqr_value
  lower_limit<-data_sum[2]-(iqr.multiplier*iqr_value)
  
  
  if(is.na(iqr_value)==FALSE){
    #if(iqr_value>0)
      {
      if(length(which(cdata<lower_limit)==TRUE)>0){
        if(replace.by.NA==TRUE){
          cdata[which(cdata<lower_limit)]<-NA
        }else{
          cdata[which(cdata<lower_limit)]<-lower_limit #min(cdata[which(cdata>lower_limit & cdata<upper_limit)],na.rm=TRUE)
          
        }
      }
      
      if(length(which(cdata>upper_limit)==TRUE)>0){
        
        if(replace.by.NA==TRUE){
          cdata[which(cdata>upper_limit)]<-NA
        }else{
          
          cdata[which(cdata>upper_limit)]<-upper_limit #max(cdata[which(cdata>lower_limit & cdata<upper_limit)],na.rm=TRUE)
        }
      }
    }
  }
  
  return(cdata)
}