build_model_logistf: build_model_logistf

In wolski/prolfqua: Proteomics Label Free Quantification

build_model_logistf

Description

build_model_logistf

Usage

build_model_logistf(data, formula)

See Also

Other modelling: Contrasts, ContrastsFirth, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, ContrastsTable, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, ModelFirth, build_model(), contrasts_fisher_exact(), generate_contrasts(), generate_contrasts_for_factor(), get_anova_df(), get_complete_model_fit(), get_p_values_pbeta(), group_label(), interaction_contrasts(), isSingular_lm(), level_specific_contrasts(), linfct_all_possible_contrasts(), linfct_factors_contrasts(), linfct_from_model(), linfct_matrix_contrasts(), main_effect_contrasts(), merge_contrasts_results(), model_analyse(), model_summary(), moderated_p_limma(), moderated_p_limma_long(), my_contest(), my_contrast(), my_contrast_V1(), my_contrast_V2(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_peptide_predictions(), process_factor(), sim_build_models_lm(), sim_build_models_lmer(), sim_build_models_logistf(), sim_make_model_lm(), sim_make_model_lmer(), strategy_logistf(), summary_ROPECA_median_p.scaled()

Examples

istar <- prolfqua::sim_lfq_data_peptide_config(Nprot = 10, with_missing = TRUE, weight_missing = 0.5, seed = 3)
istar$data <- prolfqua::encode_bin_resp(istar$data, istar$config)
tmp <- LFQData$new(istar$data, istar$config)
formula <- paste0(tmp$config$table$bin_resp , "~ group_")
xx2 <- build_model_logistf(tmp, formula)

istar <- prolfqua::sim_lfq_data_protein_config(Nprot = 10, with_missing = TRUE, weight_missing = 0.5, seed = 3)
istar$data <- prolfqua::encode_bin_resp(istar$data, istar$config)
tmp <- LFQData$new(istar$data, istar$config)
formula <- paste0(tmp$config$table$bin_resp , "~ group_")
xx <- build_model_logistf(tmp, formula)



m <- xx$models$models1$modelDF$linear_model[[1]]
linfct <- linfct_from_model(m)
linfct_all_possible_contrasts(linfct$linfct_factors)
x <- prolfqua::linfct_all_possible_contrasts(linfct$linfct_interactions)
linfct <- linfct_factors_contrasts(m)

m <- xx2$models$models2$modelDF$linear_model[[1]]
linfct <- linfct_from_model(m)
x <- linfct_all_possible_contrasts(linfct$linfct_factors)
x <- prolfqua::linfct_all_possible_contrasts(linfct$linfct_interactions)
linfct <- linfct_factors_contrasts(m)

wolski/prolfqua documentation built on June 8, 2025, 5:19 a.m.