distToNeg {phenoDist} | R Documentation

## 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.

### 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)

[Package phenoDist version 1.27.0 Index]