distToNeg: distToNeg

In phenoDist: Phenotypic distance measures

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.

Details

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

Value

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

Author(s)

Xian Zhang

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)

phenoDist documentation built on May 2, 2018, 4:46 a.m.