Nothing
#R
context("profile mode to centroid")
test_that("compare to ground truth (Orbitrap) centroids.", {
p <- .getProfileMS2()
mZ <- p$mZ
intensity <- p$intensity
n <- length(intensity)
peakgrps.groundtruth <- split(1:n, .determine.peakgroups.orbitrap(intensity))
peakgrps.groundtruth <- peakgrps.groundtruth[names(peakgrps.groundtruth) != "0"]
rv <- lapply(peakgrps.groundtruth, FUN = function(i) {
intensity.auc <- .trapez(mZ[i], intensity[i])
mZ.centroid <- weighted.mean(x = mZ[i], w = intensity[i])
data.frame(mZ = mZ.centroid, intensity = intensity.auc, n=length(i))
})
centroid.groundtruth <- do.call("rbind", rv)
# compare ten most intense peaks
topN <- 10
centroid.groundtruth.topN <- centroid.groundtruth[order(centroid.groundtruth$intensity, decreasing=TRUE)[1:topN],]
rv <- centroid(mZ, intensity, tolppm=20)
rv.topN <- rv[order(rv$intensity, decreasing=TRUE)[1:topN],]
expect_equal(
c(summary(fit <- lm(rv.topN$mZ ~ centroid.groundtruth.topN$mZ))$r.squared,
summary(fit <- lm(rv.topN$intensity ~ centroid.groundtruth.topN$intensity))$r.squared),
c(1,1), tolerance = 0.01)
})
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