PDMByWellAvg: Compute phenotypic distance matrix with well features

Description

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

Usage

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

Arguments

profiles

A data frame, containing the phenotypic profiles, as returned from the summarizeWells function of the imageHTS package.

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.

Value

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

Details

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.

Examples

Run this code


  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