Phenotypes-class: Phenotypes class.
In vladpetyuk/simMSnSet: Simulation of MSnSet Objects

Description Usage Arguments Details Methods (by generic) Slots Examples

Details about Phenotypes class.

## S4 method for signature 'Phenotypes'
show(object)

## S4 method for signature 'Phenotypes'
simulate(object, seed = NULL)

`object`	Phenotypes-class object
`seed`	an integer for `set.seed`

Class holding information about the samples

show: Show method for a Phenotype object
simulate: Selects which samples are going to be outliers given the value of the proportionOutlying slot.

n: number of samples
proportionOutlying: proportion of outlying or erroneusly assigned samples. It is not uncommong that in large-scale experiments up to ~5% samples appear as outliers.
originalPhenotypes: character vector with original or intended phenotype (group) assignment
simulatedPhenotypes: character vector with phenotype assigments after pretending that some of the samples are actually outliers
sampleNames: character vector with sample names
meanFoldChange: numeric value controlling the applitude of average fold of change between the conditions. Used as sdlog in rlnorm function.
pipettingAccuracy: a parameter for generating sample systematic biases
sampleBiases: normalization scaling factors
simulated: logical indicated if the object has been simulated

# 10 samples (5 controls + 5 cases)
# Note, the number of outlying samples is somewhat extreme - 50%.
# This is for demonstration purpose only.
ph <- Phenotypes(original=c('Ctrl', 'Ctrl', 'Ctrl', 'Ctrl', 'Ctrl',
                            'Case', 'Case', 'Case', 'Case', 'Case'),
                 proportionOutlying=0.5)
ph <- simulate(ph, seed=123)
show(ph)