PDMByWellAvg {phenoDist} | R Documentation |
This function computes the phenotypic distance matrix, with cell features averaged by well.
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
summarizeWells
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