R/group_by_isotopes_v4.R

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

group_by_isotopes_v4 <- function(dataA, step.mz.diff = 1, 
    mdgnum = -1) {
    diffmatB <- {
    }
    
    
    
    time_mult_fact <- 1
    diff_mz_num <- 1
    
    t1 <- dataA$time
    
    mzdefect <- 1000 * ((dataA$mz - floor(dataA$mz)))
    
    
    d1 <- density(mzdefect, bw = "nrd", from = min(mzdefect), 
        to = (0.01 + max(mzdefect)))
    
    time_step <- step.mz.diff * 1
    time_step <- abs(d1$x[1] - d1$x[time_step + 1])
    
    t1 <- d1$x
    
    
    gid <- {
    }
    
    gid <- paste("ISgroup", dim(dataA)[1], sep = "")
    
    
    
    # time_cor_groups<-sapply(list(myData1=dataA),function(x)
    # #print(x);split(x,cut(mzdefect,breaks=d1$x)))
    
    # time_cor_groups<-sapply(list(myData1=dataA),function(x)
    # split(x,cut(mzdefect,breaks=seq(0,1000,1))))
    
    time_cor_groups <- sapply(list(myData1 = dataA), function(x) split(x, 
        cut(mzdefect, breaks = seq(0, 1000, d1$x))))
    
    # length(time_cor_groups)
    diffmatB <- {
    }
    for (gnum in 1:length(time_cor_groups)) {
        
        cur_group <- {
        }
        
        # print(dim(time_cor_groups[[gnum]]))
        if (dim(time_cor_groups[[gnum]])[1] > 0) {
            
            ISgroup <- paste("ISgroup", mdgnum, gnum, sep = "_")
            
            # print(time_cor_groups[[gnum]])
            cur_group <- as.data.frame(time_cor_groups[[gnum]])
            cur_group <- cbind(ISgroup, cur_group)
            
            # print('cur group')
            
            # print(cur_group)
            
            if (length(cur_group) > 0) {
                # cur_group<-as.data.frame(cur_group)
                cur_group <- cur_group[order(cur_group$mz), 
                  ]
                
                # print(length(diffmatB))
                if (length(diffmatB) < 1) {
                  diffmatB <- cur_group
                } else {
                  
                  # print('here') print(dim(diffmatB))
                  # print(dim(cur_group))
                  diffmatB <- rbind(diffmatB, cur_group)
                }
                # groupnum<-groupnum+1
            }
        }
    }
    
    diffmatB <- as.data.frame(diffmatB)
    
    
    # table(diffmatB$MDgroup)
    
    if (dim(diffmatB)[1] > 0) {
        cnames <- colnames(diffmatB)
        cnames[1] <- "ISGroup"
        # print(cnames)
        colnames(diffmatB) <- cnames
    }
    
    return(diffmatB)  #$MDgroup)
}