R/maldi.R

#' Example data maldi.RData for RFtools
#'
#' This dataset is the intensity matrix generated by MALDI-TOF MS used in Rossel and Martínez Arbizu (submitted)
#' The Data shows MALDI-TOF MS spectra of 173 harpacticoid copepod specimens belonging to 16 different species from 
#' the North Sea benthic environment resulting in 176 different mass spectra. Three specimens were cut into to parts before 
#' measurement, accordingly resulting in two mass spectra per specimen. Data was generated using a Microflex LT/SH System 
#' (Bruker Daltonics) with a laser intensity between 50 to 60% in a mass range from 2000 to 20000.
#' Mass spectra were measured with flexControl 3.4 software (factory delivered Bruker Daltonics software).
#' Data was processed in R using packages MALDIquant and MALDIquantForeign, trimming mass spectra from 3000 to 15000 m/z.   
#' Spectra were smoothed (Savitzky & Golay), baseline removed (SNIP baseline estimation method) and spectra normalized using
#' TIC method. Noise was estimated using a signal to noise ratio of 7. Subsequently peaks were binned once as implemented in 
#' MALDIquant with a tolerance of 0.002 in a strict approach. The resulting intensity matrix was hellinger transformed (square root of
#' relative intensities) and is provided herewith.
#' Data was generated at Senckenberg am Meer Proteome Laboratory, German Center for Marine Biodiversity Research (DZMB), Wilhelmshaven, Germany
#' 
#' \itemize{
#'   \item code  Individual specimen code
#'   \item species  Name of the harpacticoid species
#'   \item Columns 3 to 544: m/z bins of MALDI-TOF spectrum showing hellinger transformed intensity 
#'    }
#'@docType data
#'@name maldi
#'@keywords datasets data MALDI-TOF Mass_spectra
#'@usage data(maldi)
#'@author Sven Rossel  \email{sven.rossel@@senckenberg.de} 
#'@format A data frame with 176 rows (specimens), 543 variables(protein masses) and a grouping factor (species)
#'
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pmartinezarbizu/RFtools documentation built on March 10, 2021, 12:11 p.m.