valleys: Find Peak Valleys
In MsCoreUtils: Core Utils for Mass Spectrometry Data

Description Usage Arguments Value Note Author(s) See Also Examples

This function finds the valleys around peaks.

1	valleys(x, p)

`x`	`numeric`, e.g. intensity values.
`p`	`integer`, indices of identified peaks/local maxima.

A matrix with three columns representing the index of the left valley, the peak centroid, and the right valley.

The detection of the valleys is based on localMaxima. It returns the first occurence of a local maximum (in this specific case the minimum). For plateaus, e.g. c(0, 0, 0, 1:3, 2:1, 0) this results in a wrongly reported left valley index of 1 (instead of 3, see the example section as well). In real data this should not be a real problem. x[x == min(x)] <- Inf could be used before running valleys to circumvent this specific problem but it is not really tested and could cause different problems.

Sebastian Gibb

Other extreme value functions: .peakRegionMask(), localMaxima(), refineCentroids()

ints <- c(5, 8, 12, 7, 4, 9, 15, 16, 11, 8, 3, 2, 3, 2, 9, 12, 14, 13, 8, 3)
mzs <- seq_along(ints)
peaks <- which(localMaxima(ints, hws = 3))
cols <- seq_along(peaks) + 1

plot(mzs, ints, type = "h", ylim = c(0, 16))
points(mzs[peaks], ints[peaks], col = cols, pch = 20)

v <- valleys(ints, peaks)
segments(mzs[v[, "left"]], 0, mzs[v[, "right"]], col = cols, lwd = 2)

## Known limitations for plateaus
y <- c(0, 0, 0, 0, 0, 1:5, 4:1, 0)
valleys(y, 10L) # left should be 5 here but is 1

## a possible workaround that may cause other problems
y[min(y) == y] <- Inf
valleys(y, 10L)