PDMByWellAvg {phenoDist} | R Documentation

## Compute phenotypic distance matrix with well features

### Description

This function computes the phenotypic distance matrix, with cell features averaged by well.

### Usage

      PDMByWellAvg(profiles, selectedWellFtrs, transformMethod=c('none', 'scale', 'PCA'), distMethod=c('manhattan', 'euclidean', 'correlation', 'mahalanobis'), nPCA)

### Arguments

`profiles` | A data frame, containing the phenotypic profiles, as returned from the `summarizeWells` function of the `imageHTS` package.
`selectedWellFtrs` | A character vector indicating well features to be used in the calculation. If missing, all features are used.
`transformMethod` | A character string indicating which transformation method should be used. This must be (an abbreviation of) one of the strings 'none', 'scale' or 'PCA'.
`distMethod` | A character string indicating which distance method should be used. This must be (an abbreviation of) one of the strings 'manhattan', 'euclidean', 'correlation' or 'mahalanobis'.
`nPCA` | An integer scalar for the number of PCA dimensions to be used in the calculation.

### Details

Pair-wise phenotypic distance measurements of the treatments in screen results in a phenotypic distance matrix. The features stored in `profiles` are transformed with the `transformMethod` and the distance matrix is calculated with the `distMethod`.

### Value

A symmetric distance matrix with dimensions equaling to the number of rows of `profiles`.

### Author(s)

Xian Zhang

### See Also

`summarizeWells`

### Examples

      library('phenoDist')

      ## load the imageHTS object
      load(system.file('kimorph', 'kimorph.rda', package='phenoDist'))
      x@localPath <- file.path(tempdir(), 'kimorph')

      ## calculate pair-wise svm distance matrix
      load(system.file('kimorph', 'selectedFtrs.rda', package='phenoDist'))
      pdm <- PDMByWellAvg(profiles=summarizeWells(x, getUnames(x,plate=1, row=2:3, col=3), 'conf/featurepar.txt'), selectedWellFtrs, transformMethod='scale', distMethod='euclidean')
      pdm

[Package phenoDist version 1.27.0 Index]