gcSim {gcExplorer}R Documentation

Create artificial cluster data

Description

Functionality to create artificial time course gene cluster data.

Usage

gcSim(sim=c("arima","norm","pattern","noise","outlier"), time=10,
      sd=0.1, sd.ri=0, size=50, n=10, ar=NULL, o=NULL, cent)

gcData(...)

Arguments

sim simulation method used
time number of time points
sd standard deviation of the expression profiles
sd.ri standard deviation of the random intercept or gene specific shift
size cluster size, either one value for all clusters or a vector of cluster sizes of length n
n number of clusters
ar any value between -1 and 1
o the degree of differencing
cent a data matrix giving expression profiles in rows, only used if sim="pattern" or sim="outlier"
... Several "gcSim" objects can be combined using function gcData.

Details

gcSim is a unifying function to call different data simulators.

arima generates expression patterns that come from an integrated AR-process with AR order 1 that can be controlled via ar and the degree of differencing o. sim="norm" and sim="noise" generate normally distributed expression patterns where sim="noise" is used to form a noise set of genes.

sim="pattern" and sim="outlier" can be used to generate clusters based on a set of cluster centers which are passed to the functions using the argument cent. sim="outlier" can be used to test Jackknife distance measures.

gcData can be used to combine different artificial data generators.

Value

a data matrix

Author(s)

Theresa Scharl

See Also

pattern

Examples

## generate 10 clusters with normally distributed expression patterns:
data <- gcSim(sim="norm", time=16, sd=0.1, sd.ri=0.5, 
              size=50, n=10)
matplot(t(data),type="l",pch=1)

## combine expression patterns that follow an ARIMA process and a null cluster:

data <- gcData(gcSim(sim="arima", time=16, sd=0.1, sd.ri=0.5, 
                     size=c(20,50,100,100), n=4),
               gcSim(sim="noise",time=16, size=100, sd=0))
matplot(t(data),type="l")

[Package gcExplorer version 0.9-1 Index]