R/cent_centWave.R

In nathaniel-mahieu/centWaveP: CWT Based Chromatographic Peak Detection

#' Detect regions of interest (regions of m/z vs rt space with high densitites of peaks)
#' 
#' \code{cent} returns a list of all regions of interest as rectangles in m/z vs rt space.
#' 
#' This function is a C++ implementation of the region of interest detection algorithm described in the centWave paper. The algorithm steps through scans sequentially and performs the following steps for every peak:
#' \enumerate{
#'  \item If there exists an ROI encompassing the mass, add the peak to that ROI.
#'  \item If an appropriate ROI does not exist, create a new ROI.
#'  \item Check all unfinished ROIs - if a peak hasn't been added within the previous \code{maxskip} scans save it.
#'  }
#' 
#' @param mz numeric A vector of exact mass centroids, all scans concatenated.
#' @param i numeric A vector of intensities corresponding to \code{mz}, all scans concatenated.
#' @param scanindex integer A vector of integers corresponding to the start of a new scan in the \code{mz} and \code{i} vectors.
#' @param ppm numeric the ppm mass error acceptable before a new ROI is initialized. This ppm is allowed on both sides of the mass.
#' @param prefilter numeric a two integer vector.  The first indicates the minimum number of peaks an ROI must contain to be retained.  The second indicates the minimum intensity those muct be.
#' @param maxskip integer The number of scans an ROI must not contain a peak before clossing the ROI.  \emph{This is an addition to the original algorithm. Useful for QE data.}
#' 
#' @return A list, one entry for each region of interest.  
#' 
#' 
#' @section Attribution:
#' This code was modified from the originally published centWave algorithm [1].  The code was orginally distributed and obtained under the GPL2 license via the xcms software package [2]. The original algorithms depend on the wavelet analysis code included in the MassSpecWavelet package [3]. All code herein was obtained under the GPL2 license and remains under the GPL 3 license or greater.
#' 
#' @seealso 
#' \link{\code{wave}} \link{\code{estimateBaselineNoise}}
#' 
#' [1] Tautenhahn, R., B?ttcher, C., & Neumann, S. (2008). Highly sensitive feature detection for high resolution LC/MS. BMC bioinformatics, 9(1), 1. \link[dest=http://dx.doi.org/10.1186/1471-2105-9-504]{http://dx.doi.org/10.1186/1471-2105-9-504}
#' [2] Smith, C. A., Want, E. J., O'Maille, G., Abagyan, R., & Siuzdak, G. (2006). XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Analytical chemistry, 78(3), 779-787. \link[dest=10.1021/ac051437y]{10.1021/ac051437y}
#' [3] Du, P., Kibbe, W. A., & Lin, S. M. (2006). Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. Bioinformatics, 22(17), 2059-2065. \link[dest=10.1093/bioinformatics/btl355]{10.1093/bioinformatics/btl355}
#' 
#' @export
#' 

#' @useDynLib centWaveP
#' @importFrom Rcpp sourceCpp

cent = function(mz, i, scanindex,  ppm = 2, prefilter = c(0,0), maxskip = 0) {
  #SEXP findmzROI(SEXP mz, SEXP intensity, SEXP scanindex, SEXP mzrange, SEXP scanrange, SEXP lastscan, SEXP dev, SEXP minEntries, SEXP prefilter, SEXP noise, SEXP maxskip)
  .Call("findmzROI",
    as.double(mz),
    as.double(i),
    as.integer(scanindex), 
    as.double(range(mz)),
    as.integer(c(1,length(scanindex))), 
    as.integer(length(scanindex)),
    as.double(ppm * 1E-6), 
    as.integer(0), 
    as.integer(prefilter), 
    as.integer(0), 
    as.integer(maxskip),
    PACKAGE="centWaveP")
  }