distToNeg {phenoDist} | R Documentation |
From a pair-wise distance matrix, this function extracts the corresponding distance between a sample and negative controls.
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
PDMBySvmAccuracy
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)