R/group_bymassdefect_old.R

In yufree/xMSannotator: xMSannotator: R package for network based annotation of metabolomics data.

group_bymassdefect_old <- function(dataA, pct.mz.diff = 10) {
    
    
    mzdefect <- dataA$mz - floor(dataA$mz)
    
    
    # print(mzdefect[1:10]) dataA<-cbind(dataA)
    
    # Step 1 Group features by m/zdim(data_a)[1]
    mz_groups <- lapply(1:dim(dataA)[1], function(j) {
        
        commat = {
        }
        commzA = new("list")
        commzB = new("list")
        
        getbind_same <- c(j)
        
        
        ppmb = (pct.mz.diff) * (mzdefect[j]/100)
        
        # getbind_same<-c(getbind_same,which(abs(mzdefect-mzdefect[j])<=ppmb))
        
        getbind_same <- which(abs(mzdefect - mzdefect[j]) <= 
            ppmb)
        
        
        # gid<-paste('parent',getbind_same,sep='')
        
        return(getbind_same)
        
    })
    
    
    mz_groups <- unique(mz_groups)
    
    del_list <- {
    }
    
    gid <- {
    }
    
    gid <- paste("MDgroup", dim(dataA)[1], sep = "")
    
    # length(mz_groups)
    for (m in 1:length(mz_groups)) {
        
        if ((m %in% del_list) == FALSE) {
            for (n in (m + 1):length(mz_groups)) {
                
                if (n > length(mz_groups)) {
                  break
                }
                com1 <- intersect(mz_groups[[m]], mz_groups[[n]])
                if (length(com1) > 0) {
                  
                  mz_groups[[m]] <- c(mz_groups[[m]], mz_groups[[n]])
                  del_list <- c(del_list, n)
                  mz_groups[[n]] <- c(0)
                }
            }
            
            # mz_groups[[m]][[1]]<-unique(mz_groups[[m]][[1]])
        }
    }
    if (length(del_list) > 0) {
        mz_groups <- mz_groups[-del_list]
    }
    
    gidmat <- {
    }
    for (k in 1:length(mz_groups)) {
        
        for (m in 1:length(mz_groups[[k]])) {
            
            
            gid[mz_groups[[k]][m]] <- paste("MDgroup", mz_groups[[k]][1], 
                sep = "")
            
            curres <- cbind(mz_groups[[k]][m], gid[mz_groups[[k]][m]])
            
            gidmat <- rbind(gidmat, curres)
            
        }
        
    }
    
    colnames(gidmat) <- c("mzindex", "MDgroup")
    gidmat <- as.data.frame(gidmat)
    
    return(gidmat)
    
    # return(mz_groups)
}