correctRT: Retention time correction for ALS chromatographic profiles

In rwehrens/alsace: ALS for the Automatic Chemical Exploration of mixtures

Description

Correction of retention time differences of ALS concentration profiles using parametric time warping.

Usage

correctRT(CList, reference,
                 what = c("corrected.values", "models"),
                 init.coef = c(0, 1, 0), ...)

Arguments

CList	List of matrices containing concentration profiles.
reference	Index of the sample that is to be considered the reference sample.
what	What to return: either the time-corrected profiles (useful for visual inspection) or the warping models (for further programmatic use).
init.coef	Starting values for the optimisation.
...	Optional arguments for the ptw function. The only argument that cannot be changed is warp.type: this is always equal to "global".

Value

A list of warped concentration profiles, mirroring the CList list element from the ALS object.

Author(s)

Ron Wehrens

See Also

ptw, correctPeaks

Examples

data(teaMerged)
CList.corrected <- correctRT(teaMerged$CList, reference = 2)

original.profiles <- sapply(teaMerged$CList, identity, simplify = "array")
corrected.profiles <- sapply(CList.corrected, identity, simplify = "array")

def.par <- par(no.readonly = TRUE)
par(mfrow = c(2,4))
for (i in 1:4)
    matplot(dimnames(original.profiles)[[1]],
            original.profiles[,i,], type = "l", lty = 1,
            xlab = "Time (min.)", ylab = "Response",
            main = paste("Component", i))
for (i in 1:4)
    matplot(dimnames(original.profiles)[[1]],
            corrected.profiles[,i,], type = "l", lty = 1,
            xlab = "Time (min.)", ylab = "Response",
            main = paste("Component", i, "- warped"))
par(def.par) ## reset defaults

rwehrens/alsace documentation built on May 28, 2019, 10:42 a.m.