phenoDist (version 1.20.0)

distToNeg: distToNeg

Description

From a pair-wise distance matrix, this function extracts the corresponding distance between a sample and negative controls.

Usage

distToNeg(x, distMatrix, neg='rluc')

Arguments

x

An imageHTS object

distMatrix

A pair-wise distance matrix, as generated by PDMBySvmAccuracy.

neg

A character string to identify negative controls.

Value

A numeric vector with length equal to the dimension of the distance matrix.

Details

This function averages the distance measurements between the sample and all negative controls on the same plate.

See Also

PDMBySvmAccuracy

Examples

  library('phenoDist')

  ## load the imageHTS object
  load(system.file('kimorph', 'kimorph.rda', package='phenoDist'))
  x@localPath <- file.path(tempdir(), 'kimorph')

  ## load sample phenotypic distance matrix
  load(system.file('kimorph', 'svmAccPDM_Pl1.rda', package='phenoDist'))

  ## replicate ranking
  ranking <- repDistRank(x, distMatrix=svmAccPDM_Pl1)
  summary(ranking)

  ## phenotypic distance to negative control
  pheno <- distToNeg(x, distMatrix=svmAccPDM_Pl1, neg='rluc')

  ## separation between negative and positive controls
  ctlSeparatn(x, pheno, neg='rluc', pos='ubc', method='robust')

  ## replicate correlation coefficient
  repCorr(x, pheno)