Description Usage Arguments Value Examples
Calculate the Generalized Berk-Jones test statistic and p-value.
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test_stats |
Vector of test statistics for each factor in the set (i.e. marginal test statistic for each SNP in a gene). |
cor_mat |
d*d matrix of the correlations between all the test statistics in the set, where d is the total number of test statistics in the set. You only need to specify EITHER cor_mat OR pairwise_cors. |
pairwise_cors |
A vector of all d(d-1)/2 pairwise correlations between the test statistics. You only need to specify EITHER cor_mat OR pairwise_cors. |
A list with the elements:
GBJ |
The observed Generalized Higher Criticism test statistic. |
GBJ_pvalue |
The p-value of this observed value, given the size of the set and correlation structure. |
err_code |
Sometimes if your p-value is very small (<10^(-12) usually), R/C++ do not have enough precision in their standard routines to calculate the number accurately. In these cases (and very rarely others) we switch to standard Berk-Jones instead (more stable numerically) and let you know with a message here. |
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