R/methods-other.R

In lgatto/MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

############################################################
## Methods for "basic" classes.
##

############################################################
## Methods for matrix.
##
############################################################
## removePeaks
##
## The removePeaks method for a matrix. Thus we can apply it
## to the matrix returned by mzR::peaks
## setMethod("removePeaks", "matrix", function(object, t, centroided=FALSE){
##     ## Second column is intensity.
##     if(t == "min")
##         t <- min(object[object[, 2] > 0, 2], na.rm=TRUE)
##     if(!is.numeric(t))
##         stop("'t' must either be 'min' or numeric.")
##     if(centroided){
##         object[, 2] <- utils.removePeaks_centroided(object[, 2], t)
##     }else{
##         object[, 2] <- utils.removePeaks(object[, 2], t)
##     }
##     return(object)
## })

############################################################
## clean
##
## The Spectrum's "clean" method for a matrix. The matrix is
## supposed to be returned by the mzR::peaks function, thus,
## first column will be M/Z, second intensity.
## setMethod("clean", "matrix", function(object, all=FALSE){
##     keep <- utils.clean(object[, 2], all)
##     return(object[keep, , drop=FALSE])
## })