R/rule80.R

In statTarget: Statistical Analysis of Molecular Profiles

### 80 percent rule for metabolomics data
### This function provide the 80 percent rule 
### for the missing value correction
### degree The group factor in the data
### m The data input
### A matrix with adjusted data
### A variable will be kept if it has a non-zero value 
### for at least 80 percent of each group.
### Smilde A. Fusion of mass spectrometry-based 
### metabolomics data. 2005, Anal. Chem. 77, 6729-36.
rule80 <- function(m,degree) {
  dx <- c() 
  for(i in 1:ncol(m)){
    freq <- as.vector(tapply(m[,i] , degree, function(x){
      sum(x == "0")/length(x)}))
    if(sum(freq > 0.8) > 0) dx <- c(dx , i)
  } 
  if(length(dx) >0) m <- m[,-dx]
  return(m)
}