getPeakTable {alsace} | R Documentation

## Convert MCR results into an ordered peak table

### Description

Function returns a matrix of intensities, where rows correspond to (aligned) features and columns to objects (samples, injections, ...). The function performs a complete linkage clustering of retention times across all samples, and cuts at a height given by the user (which can be interpreted as the maximal inter-cluster retention time difference). If two peaks from the same sample are assigned to the same cluster, and error message is given.

### Usage

    getPeakTable(peakList, response = c("area", "height"),
                 use.cor = TRUE, maxdiff = 0.2, plotIt = FALSE, ask = plotIt)

### 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.
`response` | An indicator whether peak area or peak height is to be used as intensity measure. Default is peak area.
`use.cor` | Logical, indicating whether to use corrected retention times (by default) or raw retention times (not advised!).
`maxdiff` | Height at which the complete linkage dendrogram will be cut. Can be interpreted as the maximal inter-cluster retention time difference.
`plotIt` | Logical. If TRUE, for every component a stripplot will be shown indicating the clustering.
`ask` | Logical. Ask before showing new plot?

### Details

If one sees warnings about peaks from the same sample sharing a cluster label, one option is to reduce the `maxdiff` variable - this, however, will increase the number of clusters. Another option is to filter the peaks on intensity: perhaps one of the two peaks in the cluster is only a very small feature.

### Value

The function returns a data frame where the first couple of columns contain meta-information on the features (component, peak, retention time) and the other columns contain the intensities of the features in the individual injections.

### Author(s)

Ron Wehrens

### Examples

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

[Package alsace version 1.23.1 Index]