alsace (version 1.8.0)

correctPeaks: Correct peak positions according to a ptw warping model

Description

Once an appropriate warping model has been established, corrected retention times can be predicted for each peak. These are stored in a separate column in the list of peak tables.

Usage

correctPeaks(peakList, modList)

Arguments

peakList

A nested list of peak tables: the first level is the sample, and the second level is the component. Every component is described by a matrix where every row is one peak, and the columns contain information on retention time, full width at half maximum (FWHM), peak width, height, and area.

modList

A list of ptw models.

Value

containing the corrected retention time.

See Also

correctRT

Examples

data(teaMerged)
pks <- getAllPeaks(teaMerged$CList, span = 11)
warping.models <- correctRT(teaMerged$CList, reference = 2,
                            what = "models")
pks.corrected <- correctPeaks(pks, warping.models)

## original profiles and peaks, in black and gray
plot(teaMerged, mat.idx = 3, what = "profiles", comp.idx = 2,
     showWindows = FALSE, col = "gray")
abline(v = pks[[3]][[2]][,"rt"])
## shifted profiles and peaks, in red and pink
CList.corrected <- correctRT(teaMerged$CList, reference = 2)
lines(as.numeric(rownames(CList.corrected[[3]])),
      CList.corrected[[3]][,2], col = "pink")
abline(v = pks.corrected[[3]][[2]][,"rt.cor"], col = "red")
## note that the rightmost peak in the uncorrected data is no longer
## within the range of the data