pairTDP {rOCEAN} | R Documentation |
Calculates the TDP over pairs; based on SEA algorithm
pairTDP(mps, n, gCT)
mps |
Matrix or vector of pairwise associations. |
n |
Number of pairs; may not be the size of p if a threshold is used to remove large p-values. |
gCT |
Parameters of the global closed testing, output of simesCT function. |
Proportion of true discoveries out of n pairs of features.
#number of features per omic data set
n_cols<-100
n_rows<-120
#random matrix of p-values
set.seed(1258)
pvalmat<-matrix(runif(n_rows*n_cols, min=0, max=1)^5, nrow=n_rows, ncol=n_cols)
#calculate CT parameters
gCT<-simesCT(mps=pvalmat, m=nrow(pvalmat)*ncol(pvalmat))
#define the two-way feature set
subpmat<-pvalmat[61:80,26:50]
#calculate pairwise TDP for feature set
pairTDP(subpmat, n=nrow(subpmat)*ncol(subpmat), gCT)