R/AnnotationbyMonoIsotopicMass.R

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

AnnotationbyMonoIsotopicMass <- function(inputmassmat, dataA, 
    queryadductlist = c("M+H"), adduct_table, max.mz.diff = 10) {
    
    # inputmassmat<-read.table('~/Documents/Emory/JonesLab/Projects/DOD/PAHs_list_dpj.txt',sep='\t',header=TRUE)
    
    # d2<-unique(d1[,1])
    
    inputmassmat <- inputmassmat[-which(duplicated(inputmassmat[, 
        2]) == TRUE), ]
    
    mz_search_list <- {
    }
    for (m in 1:dim(inputmassmat)[1]) {
        
        mz_search_list <- rbind(mz_search_list, get_mz_by_monoisotopicmass(monoisotopicmass = inputmassmat[m, 
            1], name = as.character(inputmassmat[m, 2]), 
            queryadductlist = c("positive")))
        
        
    }
    
    ghilic <- getVenn(dataA = dataA, name_a = "Experimental data", 
        name_b = "Search list", dataB = mz_search_list_1, 
        mz.thresh = max.mz.diff, time.thresh = NA, xMSanalyzer.outloc = outloc, 
        alignment.tool = NA)
    
    
    mhilic <- merge(mz_search_list, ghilic$common, by.x = "mz", 
        by.y = "mz.data.B")
    
    mhilic_2 <- merge(mhilic, hilic_data, by.x = "mz.data.A", 
        by.y = "mz")
    
    mhilic_3 <- mhilic_2[order(mhilic_2$Name), ]
    
    mhilic_3 <- mhilic_3[, -c(3, 8, 9)]
    
    cnames <- colnames(mhilic_3)
    cnames[1] <- "mz"
    cnames[2] <- "theoretical.mz"
    colnames(mhilic_3) <- as.character(cnames)
    
    # write.table(mhilic_3,file='PAH_Hilic_pos_mode_matches.txt',sep='\t',row.names=FALSE)
    
    return(mhilic_3)
    
}