To assess the significance of these scores, we compute a permutation derived false discovery rate and assign a confidence value for each projection. Specifically, to assess the significance of Eij, we permute the lincRNA knockdown samples and control samples and compute the enrichment score for each pair across all permutations. To account for the false discovery rate associated with many lincRNAs and functional sets, we use the values of all permutations directly to assess the FDR level of Eij. Specifically, to assess the FDR for each enrichment value Eij, we accumulate all the permutation values for all lincRNA knockdowns and functional sets and compute the number of values greater than Eij as well as a vector of values greater than Eij corresponding to each permutation. The FDR is computed as the average number of permuted values greater than Eij divided by the observed number greater than Eij. Using this approach, we assign an FDR value to each lincRNA knockdown by functional set and identify significant hits as those with an FDR<0.01.
