EstEpiTOC.r

#### EstEpiTOC.R

#### DESCRIPTION
#### An R-function to estimate the pcgtAge-score under the EpiTOC model. 
#### Only required input argument is a data matrix of BMIQ (or other type-2 probe correction) normalised DNAm data. 
#### Output is the pcgtAge-score for each column (sample) in the input data matrix.

#### INPUT:
#### data.m: DNAm data beta-valued matrix with rownames labeling CpGs and columns labeling samples for which a pcgtAge-score is desired
#### mode: this is an optional parameter, which can take on 2 values: "raw" or "z". If the former, function computes the pcgtAge-score 
#### as the average methylation over the represented epiTOC loci. If this option is set to "z", then the score is computed as 
#### an average of z-scores, reflecting a deviation relative to a specified reference set of samples (as specified by ref.idx)
#### ref.idx: this needs to be specified if mode="z". It is an index vector of column position of samples in data.m which should be treated as a reference.


#### OUPTUT:
#### score: a vector of pcgtAge-scores, one value for each sample of data.m

EstEpiTOC <- function(data.m,mode="raw",ref.idx=NULL){
    load("epiTOCcpgs.RData");
    common.v <- intersect(rownames(data.m),epiTOCcpgs.v);
    print(paste("Number of represented epiTOC CpGs=",length(common.v),sep=""));
    map.idx <- match(common.v,rownames(data.m));
    if(mode=="raw"){
      score.v <- colMeans(data.m[map.idx,]);
    }
    else if (mode=="z"){
      if(is.null(ref.idx)){
          print("You have selected mode=z, so please specify a reference index vector ref.idx!");
          stop;
          break;
       }
       else {
         sd.v <- apply(data.m[map.idx,ref.idx],1,sd);
         z.m <- (data.m[map.idx,] - rowMeans(data.m[map.idx,ref.idx]))/sd.v;
         score.v <- colMeans(z.m);
       }
         
     }         
        
    return(score.v);
}