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

This function performs an SVM classification between a given sample and the negative control, calculates the weight vector, and then computes the phenotypic distance matrix based on the weight vectors.

1 | ```
PDMBySvmWeightVector(x, unames, neg='rluc', selectedCellFtrs, distMethod=c('manhattan','euclidean', 'correlation','mahalanobis'), verbose=FALSE, kernel='linear', ...)
``` |

`x` |
An |

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

`neg` |
A character string to identify the 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'. |

`verbose` |
A logical scalar indicating whether progress should be reported. |

`kernel` |
The kernel argument for the |

`...` |
Additional arguments to be passed to the |

For each well, this function collects features of all cells from the well and all cells from the negative control wells, and performs a bi-class classification using Support Vector Machine (SVM). The classification weight vectors are calculated for all wells passed to `PDMByWellAvg`

to compute the phenotypic distance matrix.

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

.

Xian Zhang

1 2 3 4 5 6 7 8 9 | ```
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 <- PDMBySvmWeightVector(x, unames=getUnames(x,plate=1, row=2:3, col=3), neg='rluc', selectedCellFtrs=selectedCellFtrs, distMethod='euclidean', verbose=FALSE, cost=1, kernel='linear')
``` |

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