R/group_bymzisotopes.R

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

group_bymzisotopes <- function(dataA, max.mz.diff = 30, numisotopes = 15, 
    mdgnum = "") {
    
    dataA <- as.data.frame(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)
        
        
        
        for (isotopepattern in c(1:numisotopes)) {
            
            isotopemass = dataA$mz[j] + as.numeric(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 <- {
    }
    
    gid <- rep(paste("M", sep = ""), dim(dataA)[1])
    
    
    # if(FALSE)
    {
        # 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]])
            }
        }
        
        # del_list<-{}
        if (length(del_list) > 0) {
            mz_groups <- mz_groups[-del_list]
        }
        
    }
    
    # ignore_list<-{}
    
    if (length(mz_groups) > 1) {
        for (k in 1:length(mz_groups)) {
            
            for (m in 1:length(mz_groups[[k]])) {
                # mz_groups[[k]]<-unique(mz_groups[[k]])
                
                # gid[mz_groups[[k]][m]]<-paste('ISgroup_',mdgnum,'_',mz_groups[[k]][1],sep='')
                
                gid[mz_groups[[k]][m]] <- paste("ISgroup_", 
                  mdgnum, "_", mz_groups[[k]][1], sep = "")
                
            }
            
        }
        
    } else {
        
        for (m in 1:length(mz_groups[[1]])) {
            # mz_groups[[1]]<-unique(mz_groups[[1]])
            
            # gid[mz_groups[[k]][m]]<-paste('ISgroup_',mdgnum,'_',mz_groups[[k]][1],sep='')
            
            gid[mz_groups[[1]][m]] <- paste("ISgroup_", mdgnum, 
                "_", mz_groups[[1]][1], sep = "")
            
        }
        
        
    }
    
    gid <- cbind(gid, dataA[, c(1:2)])
    
    return(gid)
    
}