ar1analysis: Performs AR1 fitting
In cycle: Significance of periodic expression pattern in time-series data

Description Usage Arguments Value Note See Also Examples

View source: R/ar1analysis.R

Calculation of the autocorrelation coefficients genes and variance of corresponding random variables to fit gene expression time series by AR1 processes

1	ar1analysis(eset)

eset

object of the class “ExpressionSet”

List of fitted autocorrelation coefficients (alpha) for ExpressionSet features and variance (sigma2) of corresponding random variables obtained using the ar function of the stats package.

Note that this function evaluates soley the exprs matrix and no information is used from the phenoData. In particular, the ordering of samples (arrays) is the same as the ordering of the columns in the exprs matrix. Also, replicated arrays in the exprs matrix are treated as independent i.e. they should be averagered prior to analysis or placed into different distinct “ExpressionSet” objects.

ar

data(yeast) # loading the reduced CDC28 yeast set (from the Mfuzz package)

# Data preprocessing 
if (interactive()){
data(yeast) 

yeast <- filter.NA(yeast) 
# filters genes with more than 25% of the expression values missing 

yeast  <- fill.NA(yeast) 
# for illustration only; rather use knn method for replacing missing values

tmp <- ar1analysis(yeast) 
# fits AR1 process autocorrelation coefficients  

plot(density(tmp$alpha),main="Autocorrelation")

}