R/find.Unique.mzs.R

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

find.Unique.mzs <- function(dataA, dataB, mz.thresh = 10, 
    time.thresh = NA, alignment.tool = NA) {
    
    
    data_a <- as.data.frame(dataA)
    data_b <- as.data.frame(dataB)
    data_a <- unique(data_a)
    rm(dataA)
    rm(dataB)
    
    data_b <- unique(data_b)
    
    com_mz_num = 1
    unique_mz = {
    }
    ppm_v = {
    }
    rt_v = {
    }
    
    commat = {
    }
    
    col.names.dataA = colnames(data_a)
    col.names.dataB = colnames(data_b)
    
    if (is.na(alignment.tool) == FALSE) {
        if (alignment.tool == "apLCMS") {
            sample.col.start = 5
        } else {
            if (alignment.tool == "XCMS") {
                sample.col.start = 9
                col.names.dataA[1] = "mz"
                col.names.dataA[2] = "time"
                col.names.dataB[1] = "mz"
                col.names.dataB[2] = "time"
                colnames(data_a) = col.names.dataA
                colnames(data_b) = col.names.dataB
            }
            
        }
    } else {
        # stop(paste('Invalid value for alignment.tool. Please
        # use either \'apLCMS\' or \'XCMS\'', sep=''))
        
        col.names.dataA[1] = "mz"
        
        col.names.dataB[1] = "mz"
        if (is.na(time.thresh) == FALSE) {
            col.names.dataA[2] = "time"
            col.names.dataB[2] = "time"
            # print('Using the 1st columns as \'mz\' and 2nd
            # columsn as \'retention time\'')
        } else {
            # print('Using the 1st columns as \'mz\'')
        }
        colnames(data_a) = col.names.dataA
        colnames(data_b) = col.names.dataB
    }
    
    # data_a<-data_a[order(data_a$mz),]
    # data_b<-data_b[order(data_b$mz),]
    data_a <- as.data.frame(data_a)
    data_b <- as.data.frame(data_b)
    colnames(data_a) = col.names.dataA
    colnames(data_b) = col.names.dataB
    
    # create header for the matrix with common features
    if (is.na(time.thresh) == FALSE) {
        mznames = c("index.A", "mz.data.A", "time.data.A", 
            "index.B", "mz.data.B", "time.data.B", "time.difference")
    } else {
        mznames = c("index.A", "mz.data.A", "index.B", "mz.data.B")
    }
    
    overlap_res <- find.Overlapping.mzs(dataA = data_a, dataB = data_b, 
        mz.thresh, time.thresh, alignment.tool)
    
    
    
    if (length(overlap_res$index.A) > 0) {
        uniqueA <- data_a[-c(overlap_res$index.A), ]
    } else {
        uniqueA <- data_a
    }
    
    if (length(overlap_res$index.B) > 0) {
        uniqueB <- data_b[-c(overlap_res$index.B), ]
    } else {
        uniqueB <- data_b
    }
    return(list(uniqueA = uniqueA, uniqueB = uniqueB))
}