GumbelMixpValues {pathwayPCA} | R Documentation |
Calculate the p-values of test statistics from a mixture of two Weibull Extreme Value distributions.
GumbelMixpValues(tScore_vec, pathwaySize_vec, optimParams_vec)
tScore_vec |
A vector of the maximum absolute t-scores for each
pathway (returned by the |
pathwaySize_vec |
A vector of the number of genes in each pathway. |
optimParams_vec |
The NAMED vector of optimal Weibull Extreme
Value mixture distribution parameters returned by the
|
The likelihood function is equation (4) in Chen et al (2008): a
mixture of two Gumbel Extreme Value probability density functions, with
mixing proportion p. Within the code of this function, the values
mu1
, mu2
and s1
, s2
are placeholders for the
mean and precision, respectively.
See https://doi.org/10.1093/bioinformatics/btn458 for more information.
A named vector of the estimated raw p-values for each gene pathway.
OptimGumbelMixParams
; pathway_tScores
;
SuperPCA_pVals
# DO NOT CALL THIS FUNCTION DIRECTLY. # Use SuperPCA_pVals() instead. ## Not run: ### Load the Example Data ### data("colon_pathwayCollection") n_int <- lengths(colon_pathwayCollection$pathways) ### Simulate Maximum Absolute Control t-Values ### # The SuperPCA algorithm defaults to 20 threshold values; the example # pathway collection has 15 pathways. t_mat <- matrix(rt(15 * 20, df = 5), nrow = 15) absMax <- function(vec){ vec[which.max(abs(vec))] } tAbsMax_num <- apply(t_mat, 1, absMax) ### Calculate Optimal Parameters for the Gumbel Distribution ### optParams_num <- OptimGumbelMixParams( max_tControl_vec = tAbsMax_num, pathwaySize_vec = n_int ) ### Simulate Maximum Absolute t-Values ### tObs_mat <- matrix(rt(15 * 20, df = 3), nrow = 15) tObsAbsMax_num <- apply(tObs_mat, 1, absMax) ### Calculate Observed-t-score p-Values ### GumbelMixpValues( tScore_vec = tObsAbsMax_num, pathwaySize_vec = n_int, optimParams_vec = optParams_num ) ## End(Not run)