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create all possible contrasts

Source: R/tidyMS_contrasts.R
linfct_all_possible_contrasts.Rd

create all possible contrasts

Usage

linfct_all_possible_contrasts(lin_int)

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(), contrasts_fisher_exact(), get_anova_df(), get_complete_model_fit(), get_p_values_pbeta(), group_label(), impute_refit_singular(), isSingular_lm(), 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

m <- sim_make_model_lm( "interaction")
#> creating sampleName from file_name column
#> completing cases
#> completing cases done
#> setup done
linfct <- linfct_from_model(m)
xl <- prolfqua::linfct_all_possible_contrasts(linfct$linfct_factors)
xx <- prolfqua::linfct_all_possible_contrasts(linfct$linfct_interactions)
m <- sim_make_model_lm( "factor")
#> creating sampleName from file_name column
#> completing cases
#> completing cases done
#> setup done
linfct <- linfct_from_model(m)
xl <- prolfqua::linfct_all_possible_contrasts(linfct$linfct_factors)
xx <- prolfqua::linfct_all_possible_contrasts(linfct$linfct_interactions)
m <- sim_make_model_lm( "parallel2")
#> creating sampleName from file_name column
#> completing cases
#> completing cases done
#> setup done
linfct <- linfct_from_model(m)
xl <- prolfqua::linfct_all_possible_contrasts(linfct$linfct_factors)
stopifnot(all(xl == c(0,-1)))
xx <- prolfqua::linfct_all_possible_contrasts(linfct$linfct_interactions)
stopifnot(all(xx == c(0,-1)))

m <- sim_make_model_lm( "parallel3")
#> creating sampleName from file_name column
#> completing cases
#> completing cases done
#> setup done
linfct <- linfct_from_model(m)
xl <- prolfqua::linfct_all_possible_contrasts(linfct$linfct_factors)
stopifnot(all(xl == c(0,0,0,-1,0,1,0,-1,-1)))
xx <- prolfqua::linfct_all_possible_contrasts(linfct$linfct_interactions)
stopifnot(all(xl == c(0,0,0,-1,0,1,0,-1,-1)))