R/MassSpecWavelet-package.R

In zeehio/MassSpecWavelet: Peak Detection for Mass Spectrometry data using wavelet-based algorithms

#' Peak detection of mass spectrum by Wavelet transform based methods
#'
#' MassSpecWavelet R package is aimed to detect peaks on Mass Spectrometry (MS)
#' data using Continuous Wavelet Transform (CWT).
#'
#' @author Pan Du, Simon Lin
#'
#' @references Du, P., Kibbe, W.A. and Lin, S.M. (2006) Improved peak detection
#' in mass spectrum by incorporating continuous wavelet transform-based pattern
#' matching, Bioinformatics, 22, 2059-2065.
#' @keywords package
#' @examples
#'
#' data(exampleMS)
#' SNR.Th <- 3
#' peakInfo <- peakDetectionCWT(exampleMS, SNR.Th = SNR.Th)
#' majorPeakInfo <- peakInfo$majorPeakInfo
#' peakIndex <- majorPeakInfo$peakIndex
#' plotPeak(exampleMS, peakIndex, main = paste("Identified peaks with SNR >", SNR.Th))
#'
#' @useDynLib MassSpecWavelet, .registration=TRUE
"_PACKAGE"


#' An example mass spectrum
#'
#' An example mass spectrum from CAMDA 2006. All-in-1 Protein Standard II
#' (Ciphergen Cat. \# C100-0007) were measured on Ciphergen NP20 chips. There
#' are 7 polypeptides in the sample with m/z values of 7034, 12230, 16951,
#' 29023, 46671, 66433, 147300.
#'
#'
#' @name exampleMS
#' @docType data
#' @format A numeric vector represents the mass spectrum with equal sample
#' intervals.
#' @source CAMDA, CAMDA 2006 Competition Data Set. 2006, http://camda.duke.edu.
#' @keywords datasets
NULL