extractFeatures.T {sdef} | R Documentation |
The function returns the list of features in common using the hmax rule (Frequentist model).
extractFeatures.T(output.ratio, feat.names)
output.ratio |
The output object from the Frequentist model (ratio function) |
feat.names |
names of the features (e.g Affy ID for genes) |
To select a list of interesting features from the frequentist model we suggest a decision rules in the paper: the maximum of T(h)=nb genes in common/nb genes in common under the hypothesis of independence. It is pointing out the strongest deviation from independence.
The function returns an object of the class list. Each element is a matrix where the first column contains the name of the features while the other columns contain the p-values* from the experiments. It also saves a .csv file with the same information.
*instead of the p-values any other measure used to rank the features in the experiments can be used.
max |
The list of features in common selected on the basis of the threshold associated to T(hmax) |
Alberto Cassese, Marta Blangiardo
1. M.Blangiardo and S.Richardson (2007) Statistical tools for synthesizing lists of differentially expressed features in related experiments, Genome Biology, 8, R54
data = simulation(n=500,GammaA=1,GammaB=1,r1=0.5,r2=0.8, DEfirst=300,DEsecond=200,DEcommon=100) Th<- ratio(data=data$Pval) feat.names = data$names feat.lists.T <- extractFeatures.T(output.ratio=Th, feat.names=feat.names)