Man pages for kjgleason/primo
Package in R for Integrative Multi-Omics association analysis

append_Primo_objAppend a Primo object.
calc_DmatrixDensity matrix calculation
calc_fdrCalculate the empirical false discovery rate (FDR).
calc_fdr_colCalculate the empirical false discovery rate (FDR) for a...
calc_fdr_conditionalCalculate the empirical false discovery rate (FDR) after...
calc_fdr_multiCalculate the empirical false discovery rate (FDR) for each...
chiMix_pDiffDifference from nominal P-values of a chi-squared mixture.
collapse_pp_combinCollapse posterior probabilities of association for...
collapse_pp_numCollapse posterior probabilities based on number of traits of...
collapse_pp_traitCollapse posterior probabilities of association for each...
em_iterEM Iteration
e_stepE-step
e_step_withColSumsE-step, with column sums of posterior probabilities
estimate_densitiesEstimate parameters under the null and alternative densities
estimate_densities_modTEstimate parameters under the null and alternative densities
estimate_densities_pvalEstimate parameters under the alternative density
find_leadsnpsFind the lead SNP for each phenotype in each region.
make_qmatCreate association pattern matrix
m_stepM-step
PrimoEstimate posterior probabilities of association patterns.
Primo_chiMixEstimate posterior probabilities of association patterns,...
Primo_conditionalPerform conditional analysis for a specified variant.
Primo_missdata_pvalEstimate posterior probabilities for observations missing...
Primo_missdata_tstatEstimate posterior probabilities for observations missing...
Primo_modTEstimate posterior probabilities of association patterns,...
primo-packagePrimo: Package in R for Integrative Multi-Omics association...
Primo_pvalEstimate posterior probabilities of association patterns,...
Primo_tstatEstimate posterior probabilities of association patterns,...
run_conditionalSet up conditional analysis for specified variant(s) by...
run_conditional_gwasConditional analysis for known complex trait-associated...
subset_Primo_objSubset a Primo object.
kjgleason/primo documentation built on Dec. 7, 2019, 3:38 a.m.