landmarkMatrix {flowStats} | R Documentation

## Compute and cluster high density regions in 1D

### Description

This functions first identifies high-density regions for each `flowFrame` in a `flowSet` and subsequently tries to cluster these regions, yielding the landmarks matrix that needs to be supplied to `landmarkreg`. The function is considered to be internal.

### Usage

    landmarkMatrix(data, fres, parm, border=0.05, peakNr=NULL, densities =
    NULL, n = 201, indices=FALSE)

### Arguments

`data` | A `flowSet`.
`fres` | A list of `filterResultList` objects generated by a filtering opration using a `curv1Filter`. Each list item represents the results for one of the flow parameters in `parm`.
`parm` | Character scalar of flow paramater to compute landmarks for.
`border` | A numeric in `[0,1]`. Ignore all high-density regions with mean values in the extreme percentiles of the data range.
`peakNr` | Force a fixed number of peaks.
`densities` | An optional matrix of y values of the density estimates for the `flowSet`. If this is not present, density estimates will be calculated by the function.
`n` | Number of bins used for the density estimation.
`indices` | Return matrix of population indices instead of landmark locations. These indices can be used to point into the populations identified by the curv1Filter.

### Details

In order to normalize the data using the `landmarkreg` function in the `fda`, a set of landmarks has to be computed for each `flowFrame` in a `flowSet`. The number of lansmarks has to be the same for each frame. This function identifies high-density regions in each frame, computes a simple clustering and returns a matrix of landmark locations. Missing landmarks of individual frames are substituted by the mean landmark location of the respective cluster.

### Value

A matrix of landmark locations. Columns are landmarks and rows are `flowFrames`.

### Author(s)

Florian Hahne

### See Also

`landmarkreg`,`warpSet`

### Examples

    library(flowCore)
    data(GvHD)
    tmp <- list("FSC-H"=filter(GvHD[1:3], curv1Filter("FSC-H")))
    res <-  flowStats:::landmarkMatrix(GvHD[1:3], tmp, "FSC-H")

[Package flowStats version 4.0.0 Index]