ar1analysis {cycle} | R Documentation |
Calculation of the autocorrelation coefficients genes and variance of corresponding random variables to fit gene expression time series by AR1 processes
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.
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") }