R/pmdanno.R

In pmd: Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted Analysis and Reactomics Analysis

#' read in MSP file as list for ms/ms annotation
#' @param file the path to your MSP file
#' @param digits mass or mass to charge ratio accuracy for pmd, default 2
#' @param icf intensity cutoff, default 10 percentage
#' @return list a list with MSP information for MS/MS annotation
#' @export
getms2pmd <- function(file, digits = 2, icf = 10) {
        # this part is modified from compMS2Miner's code: https://github.com/WMBEdmands/compMS2Miner/blob/ee20d3d632b11729d6bbb5b5b93cd468b097251d/R/metID.matchSpectralDB.R
        msp <- readLines(file)
        # remove empty lines
        msp <- msp[msp != '']
        ncomp <- grep('^NAME:', msp, ignore.case = TRUE)
        splitFactorTmp <-
                rep(seq_along(ncomp), diff(c(ncomp, length(msp) + 1)))

        li <- split(msp, f = splitFactorTmp)
        getmsp <- function(x) {
                namet <- x[grep('^NAME:', x, ignore.case = TRUE)]
                name <-
                        gsub('^NAME: ', '', namet, ignore.case = TRUE)
                prect <-
                        x[grep(
                                '^PRECURSORMZ: |^PRECURSOR M/Z: |^PRECURSOR MZ: |^PEPMASS: ',
                                x,
                                ignore.case = TRUE
                        )]
                prec <-
                        as.numeric(
                                gsub(
                                        '^PRECURSORMZ: |^PRECURSOR M/Z: |^PRECURSOR MZ: |^PEPMASS: ',
                                        '',
                                        prect,
                                        ignore.case = TRUE
                                )
                        )
                npt <-
                        x[grep('^Num Peaks: ', x, ignore.case = TRUE)]
                np <-
                        gsub('^Num Peaks: ', '', npt, ignore.case = TRUE)
                if (as.numeric(np) > 0) {
                        # matrix of masses and intensities
                        massIntIndx <-
                                which(grepl('^[0-9]', x) &
                                              !grepl(': ', x))
                        massesInts <-
                                unlist(strsplit(x[massIntIndx], '\t| '))
                        massesInts <-
                                as.numeric(massesInts[grep('^[0-9].*[0-9]$|^[0-9]$',
                                                           massesInts)])
                        # if any NAs remove from indx
                        mz <-
                                massesInts[seq(1, length(massesInts), 2)]
                        ins <-
                                massesInts[seq(2, length(massesInts), 2)]
                        ins <- ins / max(ins) * 100
                        msms <- cbind.data.frame(mz = mz, ins = ins)
                        msms <- msms[msms$ins > icf,]
                        dis <-
                                stats::dist(msms$mz, method = "manhattan")
                        diff <-
                                round(as.numeric(dis), digits = digits)
                        diff <- diff[order(diff)]
                        return(list(
                                name = name,
                                prec = prec,
                                msms = msms,
                                pmd = diff
                        ))
                } else{
                        return(list(
                                name = name,
                                prec = prec,
                                msms = NULL,
                                pmd = NULL
                        ))
                }

        }
        li <- lapply(li, getmsp)
        name <- vapply(li, function(x)
                x$name,'c')
        mz <- vapply(li, function(x)
                x$prec,1)
        msms <- lapply(li, function(x)
                x$pmd)
        msmsraw <- lapply(li, function(x)
                x$msms)
        return(list(
                name = unname(name),
                mz = unname(mz),
                msms = unname(msms),
                msmsraw = unname(msmsraw)
        ))
}

#' read in MSP file as list for EI-MS annotation
#' @param file the path to your MSP file
#' @param digits mass or mass to charge ratio accuracy for pmd, default 0
#' @param icf intensity cutoff, default 10 percentage
#' @return list a list with MSP information for EI-MS annotation
#' @export
getmspmd <- function(file, digits = 2, icf = 10) {
        # this part is modified from compMS2Miner's code: https://github.com/WMBEdmands/compMS2Miner/blob/ee20d3d632b11729d6bbb5b5b93cd468b097251d/R/metID.matchSpectralDB.R
        msp <- readLines(file)
        # remove empty lines
        msp <- msp[msp != '']
        ncomp <- grep('^NAME:', msp, ignore.case = TRUE)
        splitFactorTmp <-
                rep(seq_along(ncomp), diff(c(ncomp, length(msp) + 1)))

        li <- split(msp, f = splitFactorTmp)
        getmsp <- function(x) {
                namet <- x[grep('^NAME:', x, ignore.case = TRUE)]
                name <-
                        gsub('^NAME: ', '', namet, ignore.case = TRUE)
                npt <-
                        x[grep('^Num Peaks: ', x, ignore.case = TRUE)]
                np <-
                        gsub('^Num Peaks: ', '', npt, ignore.case = TRUE)
                if (as.numeric(np) > 0) {
                        # matrix of masses and intensities
                        massIntIndx <-
                                which(grepl('^[0-9]', x) &
                                              !grepl(': ', x))
                        massesInts <-
                                unlist(strsplit(x[massIntIndx], '\t| '))
                        massesInts <-
                                as.numeric(massesInts[grep('^[0-9].*[0-9]$|^[0-9]$',
                                                           massesInts)])
                        # if any NAs remove from indx
                        mz <-
                                massesInts[seq(1, length(massesInts), 2)]
                        ins <-
                                massesInts[seq(2, length(massesInts), 2)]
                        ins <- ins / max(ins) * 100
                        msms <- cbind.data.frame(mz = mz, ins = ins)
                        msms <- msms[msms$ins > icf,]
                        dis <-
                                stats::dist(msms$mz, method = "manhattan")
                        diff <-
                                round(as.numeric(dis), digits = digits)
                        diff <- diff[order(diff)]
                        return(list(
                                name = name,
                                msms = msms,
                                pmd = diff
                        ))
                } else{
                        return(list(
                                name = name,
                                msms = NULL,
                                pmd = NULL
                        ))
                }
        }
        li <- lapply(li, getmsp)
        name <- vapply(li, function(x)
                x$name,'v')
        msms <- lapply(li, function(x)
                x$pmd)
        msmsraw <- lapply(li, function(x)
                x$msms)
        return(list(
                name = unname(name),
                msms = unname(msms),
                msmsraw = unname(msmsraw)
        ))
}