Package: qch 2.0.0

Tristan Mary-Huard

qch: Query Composite Hypotheses

Provides functions for the joint analysis of Q sets of p-values obtained for the same list of items. This joint analysis is performed by querying a composite hypothesis, i.e. an arbitrary complex combination of simple hypotheses, as described in Mary-Huard et al. (2021) <doi:10.1093/bioinformatics/btab592> and De Walsche et al.(2023) <doi:10.1101/2024.03.17.585412>. In this approach, the Q-uplet of p-values associated with each item is distributed as a multivariate mixture, where each of the 2^Q components corresponds to a specific combination of simple hypotheses. The dependence between the p-value series is considered using a Gaussian copula function. A p-value for the composite hypothesis test is derived from the posterior probabilities.

Authors:Tristan Mary-Huard [aut, cre], Annaig De Walsche [aut], Franck Gauthier [ctb]

qch_2.0.0.tar.gz
qch_2.0.0.tar.gz(r-4.5-noble)qch_2.0.0.tar.gz(r-4.4-noble)
qch_2.0.0.tgz(r-4.4-emscripten)qch_2.0.0.tgz(r-4.3-emscripten)
qch.pdf |qch.html
qch/json (API)

# Install 'qch' in R:
install.packages('qch', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • PvalSets - Synthetic example to illustrate the main qch functions
  • PvalSets_cor - Synthetic example to illustrate the main qch functions using gaussian copula

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openblascppopenmp

1.00 score 174 downloads 5 exports 54 dependencies

Last updated 9 months agofrom:cbf2b368ab. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 25 2024
R-4.5-linux-x86_64OKNov 25 2024

Exports:GetH1AtLeastGetH1EqualGetHconfigqch.fitqch.test

Dependencies:ADGofTestclicolorspacecopuladplyrfansifarverFNNgenericsggplot2gluegslgtableisobandkernlabKernSmoothkslabelinglatticelifecyclemagrittrMASSMatrixmclustmgcvmulticoolmunsellmvtnormnlmenumDerivpcaPPpillarpkgconfigplyrpracmapsplinepurrrqvalueR6RColorBrewerRcppRcppArmadilloreshape2rlangscalesstablediststringistringrtibbletidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Gaussian copula density for each Hconfiguration.Copula.Hconfig_gaussian_density
EM calibration in the case of the gaussian copula (unsigned)EM_calibration_gaussian
EM calibration in the case of the gaussian copula (unsigned) with memory managementEM_calibration_gaussian_memory
EM calibration in the case of conditional independenceEM_calibration_indep
EM calibration in the case of conditional independence with memory management (unsigned)EM_calibration_indep_memory
Signed case function: Separate f1 into f+ and f-f1_separation_signed
FastKerFdr signedFastKerFdr_signed
FastKerFdr unsignedFastKerFdr_unsigned
Computation of the sum sum_c(w_c*psi_c) using Gaussian copula parallelized versionfHconfig_sum_update_gaussian_copula_ptr_parallel
Computation of the sum sum_c(w_c*psi_c) parallelized versionfHconfig_sum_update_ptr_parallel
Gaussian copula densitygaussian_copula_density
Specify the configurations corresponding to the composite H_1 test "AtLeast".GetH1AtLeast
Specify the configurations corresponding to the composite H_1 test "Equal".GetH1Equal
Generate the H_0/H_1 configurations.GetHconfig
Update of the prior estimate in EM algo parallelized versionprior_update_arma_ptr_parallel
Update of the prior estimate in EM algo using Gaussian copula, parallelized versionprior_update_gaussian_copula_ptr_parallel
Synthetic example to illustrate the main qch functionsPvalSets
Synthetic example to illustrate the main qch functions using gaussian copulaPvalSets_cor
Infer posterior probabilities of H_0/H_1 configurations.qch.fit
Perform composite hypothesis testing.qch.test
Update the estimate of R correlation matrix of the gaussian copula, parallelized versionR_MLE_update_gaussian_copula_ptr_parallel
Gaussian copula correlation matrix Maximum Likelihood estimator.R.MLE
Check the Gaussian copula correlation matrix Maximum Likelihood estimatorR.MLE.check
Gaussian copula correlation matrix Maximum Likelihood estimator (memory handling)R.MLE.memory