correctRT {alsace} | R Documentation

## Retention time correction for ALS chromatographic profiles

### 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

[Package alsace version 1.26.0 Index]