Experiment-class: Experiment class.

In vladpetyuk/simMSnSet: Simulation of MSnSet Objects

Description

Details about Experiment class.

Usage

## S4 method for signature 'Experiment'
image(x, ...)

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

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

Arguments

x	Experiment-class object
...	currently ignored
object	Experiment-class object
seed	an integer for set.seed

Details

The central class of simMSnSet package

Methods (by generic)

• image: Showing simulated experiment as an image

• show: Show method for an Experiment object

• simulate: Simulates the entire experiment

Slots

phenotypes

Phenotypes and Samples

proteins

Peptides and Proteins

simFinal

simulated final intensities

simNoise

simulated noise of intensity measurements

simMeans

simulated actual fold of changes for each peptide/sample

simSampleBiases

simulated systematic biases due to pipetting errors

simOutliers

indexes of simulated outlying samples

simMissing

index of missing measurements

simulated

A logical flag indicating if the experiment has been simulated or not

See Also

Other Experiment.class: as

Examples

# 10 proteins measured across 6 samples (3 controls + 3 cases)
pr <- Proteins(nProt=10)
ph <- Phenotypes(originalPhenotypes=c('Control', 'Control', 'Control',
                            'Case', 'Case', 'Case'))
ex <- Experiment(pr, ph)
ex <- simulate(ex)
image(ex)

vladpetyuk/simMSnSet documentation built on May 3, 2019, 6:16 p.m.