get mean methylation per group from a methylBase object

meanMethGroup.R

# returns a matrix of mean methylation values for groups defined
# by treatment vector in the methylBase obj
meanMethGroup<-function(methylBase.obj,weighted=TRUE ){
  
  data=getData(methylBase.obj) # get data frame part of the object
  treatment=methylBase.obj@treatment # get the treatment vector from the object
  
  # create the the empty resulting matrix
  result=matrix(0,ncol=length(unique(methylBase.obj@treatment)) ,nrow=nrow(methylBase.obj)  )
  colnames(result)=paste('group',unique(treatment),sep='') # column names are from treatmet vector
  
  
  for(i in 1:length(unique(treatment)) ){
    
    # get C index
    [email protected][methylBase.obj@treatment==unique(treatment)[i]]
    
    if(weighted){
      result[,i]=100*rowSums(data[,Cind,drop=FALSE],na.rm=TRUE)/rowSums(data[,Cind-1,drop=FALSE],na.rm=TRUE) # get weigthed means
    }
    else{
      result[,i]=100*rowMeans(data[,Cind,drop=FALSE]/data[,Cind-1,drop=FALSE],na.rm=TRUE)  # get means of percent methylation values
      
    }
  }
  result
}