Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/phenotypeIdentification.R

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

1 | ```
distToNeg(x, distMatrix, neg='rluc')
``` |

`x` |
An |

`distMatrix` |
A pair-wise distance matrix, as generated by |

`neg` |
A character string to identify negative controls. |

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

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

Xian Zhang

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ```
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)
``` |

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