R/group_bymzisotopes3.R

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

group_bymzisotopes3 <- function(dataA, max.mz.diff = 30, 
    numisotopes = 4) {
    
    
    
    # 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)
        
        
        
        for (isotopepattern in c(1:numisotopes)) {
            
            isotopemass = dataA$mz[j] + isotopepattern
            
            ppmb = (max.mz.diff) * (isotopemass/1e+06)
            
            getbind_same <- c(getbind_same, which(abs(dataA$mz - 
                isotopemass) <= ppmb))
            
            
            
        }
        
        
        # gid<-paste('parent',getbind_same,sep='')
        
        return(getbind_same)
        
    })
    
    
    del_list <- {
    }
    
    gid <- {
    }
    
    # length(mz_groups)
    for (k in 1:length(mz_groups)) {
        
        
        if ((k %in% del_list) == FALSE) {
            for (n in (k + 1):length(mz_groups)) {
                
                if (n > length(mz_groups)) {
                  break
                }
                com1 <- intersect(mz_groups[[k]], mz_groups[[n]])
                if (length(com1) > 0) {
                  
                  mz_groups[[k]] <- c(mz_groups[[k]], 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]
        }
    }
    
    for (k in 1:length(mz_groups)) {
        
        for (m in 1:length(mz_groups[[k]])) {
            
            
            gid[mz_groups[[k]][m]] <- paste("M", mz_groups[[k]][1], 
                sep = "")
            
        }
        
    }
    
    
    # return(gid)
    
    return(mz_groups)
}