#' Filter peak list of MSI data
#' @inheritParams filterPeaks
#' @export
filterPeaks.msimat <- function(d,
how=c("topX","XofTop","XofTotal"),
x=NULL,
index=NULL) {
df <- data.frame(peaks=d$peaks,
intensities=d$peakintensities)
outidx <- filterPeaks(d=df,
how=how,
x=x,
index=TRUE)
outidx <- outidx[order(d$peaks[outidx],decreasing=FALSE)]
newpeaks <- d$peaks[outidx]
newmat <- d$mat[,outidx]
newpeakintensities <- d$peakintensities[outidx]
out <- list(mat=newmat,
peaks=newpeaks,
spots=d$spots,
peakintensities=newpeakintensities)
class(out) <- "msimat"
return(out)
}
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