PDMByKS {phenoDist} | R Documentation |
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.
PDMByKS(x, unames, neg='rluc', selectedCellFtrs, distMethod=c('manhattan', 'euclidean', 'correlation', 'mahalanobis'))
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
ks.test
, PDMByWellAvg
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