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Fishers exact test on a datframe

Source: R/tidyMS_moderation.R
contrasts_fisher_exact.Rd

Fishers exact test on a datframe

Usage

contrasts_fisher_exact(
  fisher_input,
  observedA = "observedA",
  observedB = "observedB",
  samplesA = "samplesA",
  samplesB = "samplesB"
)

See also

Other modelling: AnovaExtractor, Contrasts, ContrastsDEqMSFacade, ContrastsDEqMSVoomFacade, ContrastsFirth, ContrastsFirthFacade, ContrastsLMFacade, ContrastsLMImputeFacade, ContrastsLMMissingFacade, ContrastsLimma, ContrastsLimmaFacade, ContrastsLimmaImputeFacade, ContrastsLimmaVoomFacade, ContrastsLimmaVoomImputeFacade, ContrastsLimpaFacade, ContrastsLmerFacade, ContrastsMissing, ContrastsModerated, ContrastsModeratedDEqMS, ContrastsPlotter, ContrastsRLMFacade, ContrastsROPECA, ContrastsROPECAFacade, ContrastsTable, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, ModelFirth, ModelLimma, StrategyLM, StrategyLimma, StrategyLimpa, StrategyLmer, StrategyLogistf, StrategyRLM, build_contrast_analysis(), build_model(), build_model_glm_peptide(), build_model_glm_protein(), build_model_impute(), build_model_limma(), build_model_limma_impute(), build_model_limma_voom(), build_model_limma_voom_impute(), build_model_limpa(), build_model_logistf(), compute_borrowed_variance(), compute_borrowed_variance_limma(), compute_contrast(), compute_lmer_contrast(), get_anova_df(), get_complete_model_fit(), get_p_values_pbeta(), group_label(), impute_refit_singular(), isSingular_lm(), linfct_all_possible_contrasts(), linfct_factors_contrasts(), linfct_from_model(), linfct_matrix_contrasts(), merge_contrasts_results(), model_analyse(), model_summary(), moderated_p_deqms(), moderated_p_deqms_long(), moderated_p_limma(), moderated_p_limma_long(), new_lm_imputed(), pivot_model_contrasts_2_Wide(), plot_lmer_peptide_predictions(), sim_build_models_lm(), sim_build_models_lmer(), sim_build_models_logistf(), sim_make_model_lm(), sim_make_model_lmer(), strategy_limma(), strategy_limpa(), strategy_logistf(), summary_ROPECA_median_p.scaled()

Examples

Nprot <- 1000
condA <- 8
condB <- 8
observedA <- sample(0:8, Nprot, replace = TRUE)
observedB <- sample(0:8, Nprot, replace = TRUE)
fisher_input <- data.frame(observedA = observedA, observedB = observedB)

fisher_input$samplesA <- condA
fisher_input$samplesB <- condB
proteinID <- unique(stringi::stri_rand_strings(Nprot + 20,5))[1:Nprot]
fisher_input$proteinID <- proteinID
res <- contrasts_fisher_exact(fisher_input)