PDMByKS {phenoDist} | R Documentation

## Compute phenotypic distance matrix by Kolmogorov-Smirnov statistics

### Description

This function calculates the Kolmogorov-Smirnov statistic between a given sample and the negative control, for each feature, and then computes the phenotypic distance matrix based on the Kolmogorov-Smirnov statistics.

### Usage

    PDMByKS(x, unames, neg='rluc', selectedCellFtrs, distMethod=c('manhattan', 'euclidean', 'correlation', 'mahalanobis'))

### Arguments

`x` | An `imageHTS` object.
`unames` | A character vector, containing the well names from where to collect the cell features. See `getUnames` for details.
`neg` | A character string to identify negative controls.
`selectedCellFtrs` | A character vector for cell features to be used in the calculation. If missing, all features are used.
`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'.

### Details

For each well, this function collects features of all cells, and performs a Kolmogorov-Smirnov test for each feature against the corresponding cell features from negative control wells, with the function `ks.test` of the `stats` package. The Kolmogorov-Smirnov statistics are collected for all wells and passed to `PDMByWellAvg` to calculate the phenotypic distance matrix.

### Value

A symmetric distance matrix with the number of rows equaling to the length of `unames`.

### Author(s)

Xian Zhang

### See Also

`ks.test`, `PDMByWellAvg`

### 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 <- PDMByKS(x, unames=getUnames(x,plate=1, row=2:3, col=3), neg='rluc', selectedCellFtrs=selectedCellFtrs, distMethod='euclidean')
      pdm

[Package phenoDist version 1.27.0 Index]