R/overlapmzchild.R

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

overlapmzchild <- function(j, mz.thresh = 10, time.thresh = NA, 
    data_a, data_b) {
    
    commat = {
    }
    commzA = new("list")
    commzB = new("list")
    ppmb = (mz.thresh) * (data_a$mz[j]/1e+06)
    
    getbind_same <- which(abs(data_b$mz - data_a$mz[j]) <= 
        ppmb)
    
    if (is.na(time.thresh) == FALSE) {
        if (length(getbind_same) > 0) {
            nearest_time_diff = 10000
            bestmatch = {
            }
            rnames = {
            }
            temp = {
            }
            commat = {
            }
            # for (comindex in 1:length(getbind_same))
            # chemscoremat_conf_levels<-foreach(c=1:length(chemids),
            # .combine=rbind) %dopar%
            commat <- lapply(1:length(getbind_same), function(comindex) {
                tempA = cbind(j, data_a[j, c(1, 2)])
                tempB = cbind(getbind_same[comindex], data_b[getbind_same[comindex], 
                  c(1, 2)])
                temp = cbind(tempA, tempB)
                
                timediff = abs(data_a[j, 2] - data_b[getbind_same[comindex], 
                  2])
                
                temp <- cbind(temp, timediff)
                
                if (timediff < time.thresh && timediff <= 
                  nearest_time_diff) {
                  bestmatch = as.data.frame(temp)
                  nearest_time_diff = timediff
                  
                  
                  
                  
                  
                  temp <- as.data.frame(temp)
                  # commat<-rbind(commat,temp)
                  # rnamestemp<-paste('mz',j,'_',comindex,sep='')
                  # rnames<-c(rnames,rnamestemp)
                }
                return(temp)
            })
            
            commat <- ldply(commat, rbind)
            
            # commat=as.data.frame(bestmatch)
            
            # if(length(commat)>=4){ rownames(commat)=rnames }
            
            
        }
    } else {
        if (length(getbind_same) > 0) {
            temp1 <- {
            }
            # for (comindex in 1:length(getbind_same))
            commat <- lapply(1:length(getbind_same), function(comindex) {
                tempA = cbind(j, data_a[j, c(1)])
                tempB = cbind(getbind_same[comindex], data_b[getbind_same[comindex], 
                  c(1)])
                temp = cbind(tempA, tempB)
                temp <- as.data.frame(temp)
                # temp=cbind(j,data_a[j,c(1)],getbind_same[comindex],data_b[getbind_same[comindex],c(1)])
                # temp1<-rbind(temp1,temp)
                return(temp)
            })
            
            commat <- ldply(commat, rbind)
            commat = as.data.frame(commat)
            # rnames<-paste('mz',j,'_',seq(1,length(getbind_same)),sep='')
            # rownames(commat)=rnames
            
        }
    }
    return(as.data.frame(commat))
    
    
    
}