Description Usage Arguments Details Value Author(s) See Also Examples

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.

1 |

`x` |
An |

`unames` |
A character vector, containing the well names from where to collect the cell features. See |

`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'. |

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.

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

.

Xian Zhang

1 2 3 4 5 6 7 8 9 10 | ```
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
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.