R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Retention time correction for ALS chromatographic profiles

correctRT

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

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(alsace)
Loading required package: ALS
Loading required package: nnls
Loading required package: Iso
Iso 0.0-17
Loading required package: ptw
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/alsace/correctRT.Rd_%03d_medium.png", width=480, height=480)
> ### Name: correctRT
> ### Title: Retention time correction for ALS chromatographic profiles
> ### Aliases: correctRT
> ### Keywords: manip
> 
> ### ** 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
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>