R/find.Unique.mzs.R

In yufree/xMSanalyzer: xMSanalyzer: R package for data analysis, comparison, and annotation of metabolomics data.

#' find.Unique.mzs
#' 
#' This function finds unique m/zs between two datasets.
#' 
#' The find.Unique.mzs function operates on two sets of feature lists with m/z
#' for each feature, denoted by L1 and L2, and iterates over all m/z values in
#' L1 to find those that are within a user defined m/z (ppm) threshold in L2.
#' 
#' @param dataA apLCMS or XCMS feature table for dataset A
#' @param dataB apLCMS or XCMS feature table for dataset B
#' @param mz.thresh Maximum m/z difference (+/-) ppm
#' @param time.thresh Maximum retention time difference (+/-) seconds
#' @param alignment.tool Name of the feature alignment tool eg: "apLCMS" or
#' "XCMS" or "NA" Use "NA" if the input matrix includes only m/z or both m/z
#' and retnetion time values.
#' @return A list is returned: \item{uniqueA }{Unique m/zs in dataA}
#' \item{uniqueB }{Unique m/zs in dataB}
#' @author Karan Uppal <kuppal2@@emory.edu>
#' @seealso apLCMS.align, XCMS.align, find.Overlapping.mzs
#' @keywords ~unique
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))
}