build_model_logistf
See also
Other modelling:
AnovaExtractor,
Contrasts,
ContrastsDEqMSFacade,
ContrastsDEqMSVoomFacade,
ContrastsFacadeBase,
ContrastsFirth,
ContrastsFirthFacade,
ContrastsFirthNestedFacade,
ContrastsLMFacade,
ContrastsLMImputeFacade,
ContrastsLMMissingFacade,
ContrastsLimma,
ContrastsLimmaFacade,
ContrastsLimmaImputeFacade,
ContrastsLimmaVoomFacade,
ContrastsLimmaVoomImputeFacade,
ContrastsLimpaFacade,
ContrastsLimpaNestedFacade,
ContrastsLmerNestedFacade,
ContrastsMissing,
ContrastsModerated,
ContrastsModeratedDEqMS,
ContrastsPlotter,
ContrastsRLMFacade,
ContrastsROPECA,
ContrastsROPECANestedFacade,
ContrastsRfitFacade,
ContrastsRfitImputeFacade,
ContrastsTable,
INTERNAL_FUNCTIONS_BY_FAMILY,
LR_test(),
Model,
ModelFirth,
ModelLimma,
StrategyLM,
StrategyLimma,
StrategyLimpa,
StrategyLmer,
StrategyLogistf,
StrategyRLM,
StrategyRfit,
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(),
compute_borrowed_variance(),
compute_borrowed_variance_limma(),
compute_contrast(),
compute_lmer_contrast(),
df.residual.rfit_prolfqua(),
get_anova_df(),
get_complete_model_fit(),
get_p_values_pbeta(),
group_label(),
impute_from_model(),
impute_refit_singular(),
linfct_from_model(),
linfct_matrix_contrasts(),
list_facades(),
lookup_facade(),
merge_contrasts_results(),
model_analyse(),
model_summary(),
moderated_p_deqms(),
moderated_p_deqms_long(),
moderated_p_limma(),
new_imputed_model(),
pivot_model_contrasts_to_wide(),
register_facade(),
sigma.rfit_prolfqua(),
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(),
vcov.rfit_prolfqua()
Examples
istar <- prolfqua::sim_lfq_data_peptide_config(Nprot = 10, with_missing = TRUE,
weight_missing = 0.5, seed = 3)
#> creating sampleName from file_name column
#> completing cases
#> completing cases done
#> setup done
istar$data <- prolfqua::encode_bin_resp(LFQData$new(istar$data, istar$config))
istar$config$bin_resp <- "bin_resp"
tmp <- LFQData$new(istar$data, istar$config)
formula <- paste0(tmp$get_config()$bin_resp , "~ group_")
xx2 <- build_model_logistf(tmp, formula)
#> Joining with `by = join_by(protein_Id)`
#> Joining with `by = join_by(protein_Id)`
istar <- prolfqua::sim_lfq_data_protein_config(Nprot = 10, with_missing = TRUE,
weight_missing = 0.5, seed = 3)
#> creating sampleName from file_name column
#> completing cases
#> completing cases done
#> setup done
istar$data <- prolfqua::encode_bin_resp(LFQData$new(istar$data, istar$config))
istar$config$bin_resp <- "bin_resp"
tmp <- LFQData$new(istar$data, istar$config)
formula <- paste0(tmp$get_config()$bin_resp , "~ group_")
xx <- build_model_logistf(tmp, formula)
#> Joining with `by = join_by(protein_Id)`
contrasts <- c(AvsB = "group_A - group_B")
m <- xx$models$models1$model_df$linear_model[[1]]
linfct_matrix_contrasts(linfct_from_model(m)$linfct_factors, contrasts)
#> (Intercept) group_B group_Ctrl
#> AvsB 0 -1 0
m <- xx2$models$models2$model_df$linear_model[[1]]
linfct_matrix_contrasts(linfct_from_model(m)$linfct_factors, contrasts)
#> (Intercept) group_B group_Ctrl peptide_IdFLq7LKTq peptide_IdJYhOpuPH
#> AvsB 0 -1 0 0 0
#> peptide_IdLiw5EMKP peptide_IdVcatZJTa peptide_IdjrLUqOjg
#> AvsB 0 0 0
#> peptide_Idq2jTaC1y
#> AvsB 0