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

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

1 | ```
PDMByWellAvg(profiles, selectedWellFtrs, transformMethod=c('none', 'scale', 'PCA'), distMethod=c('manhattan', 'euclidean', 'correlation', 'mahalanobis'), nPCA)
``` |

`profiles` |
A data frame, containing the phenotypic profiles, as returned from the |

`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. |

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`

.

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

.

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 <- PDMByWellAvg(profiles=summarizeWells(x, getUnames(x,plate=1, row=2:3, col=3), 'conf/featurepar.txt'), selectedWellFtrs, transformMethod='scale', distMethod='euclidean')
pdm
``` |

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