pairTDP: pairwise true discoveries proportion

In rOCEAN: Two-Way Feature Set Testing for Multi-Omics

pairwise true discoveries proportion

Description

Calculates the TDP over pairs; based on SEA algorithm

Usage

pairTDP(mps, n, gCT)

Arguments

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.

Value

Proportion of true discoveries out of n pairs of features.

See Also

SEA, simesCT

Examples

#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)

rOCEAN documentation built on April 12, 2025, 2:30 a.m.