R/tidyMS_R6_Modelling.R
my_contrast_V1.Rdhandles incomplete models by setting coefficients to 0
my_contrast_V1(incomplete, linfct, confint = 0.95)linear function
confidence interval default 0.95
linear model generated using lm
Other modelling:
Contrasts,
ContrastsMissing,
ContrastsModerated,
ContrastsPlotter,
ContrastsProDA,
ContrastsROPECA,
ContrastsTable,
INTERNAL_FUNCTIONS_BY_FAMILY,
LR_test(),
Model,
build_model(),
contrasts_fisher_exact(),
get_anova_df(),
get_complete_model_fit(),
get_p_values_pbeta(),
isSingular_lm(),
linfct_all_possible_contrasts(),
linfct_factors_contrasts(),
linfct_from_model(),
linfct_matrix_contrasts(),
merge_contrasts_results(),
model_analyse(),
model_summary(),
moderated_p_limma(),
moderated_p_limma_long(),
my_contest(),
my_contrast(),
my_contrast_V2(),
my_glht(),
pivot_model_contrasts_2_Wide(),
plot_lmer_peptide_predictions(),
sim_build_models_lm(),
sim_build_models_lmer(),
sim_make_model_lm(),
sim_make_model_lmer(),
strategy_lmer(),
summary_ROPECA_median_p.scaled()
m <- sim_make_model_lm( "factors")
#> creating sampleName from fileName column
#> completing cases
#> Joining with `by = join_by(protein_Id)`
linfct <- linfct_from_model(m)$linfct_factors
my_contrast_V1(m, linfct, confint = 0.95)
#> lhs sigma df estimate std.error statistic p.value
#> BackgroundX BackgroundX 1.557675 13 18.63959 0.5507212 33.84577 4.612815e-14
#> BackgroundZ BackgroundZ 1.557675 13 18.19440 0.5507212 33.03740 6.294815e-14
#> TreatmentA TreatmentA 1.557675 13 18.75377 0.5507212 34.05311 4.264271e-14
#> TreatmentB TreatmentB 1.557675 13 18.08021 0.5507212 32.83007 6.825487e-14
#> conf.low conf.high
#> BackgroundX 17.44983 19.82935
#> BackgroundZ 17.00464 19.38416
#> TreatmentA 17.56401 19.94353
#> TreatmentB 16.89045 19.26998
my_contrast_V1(m, linfct, confint = 0.99)
#> lhs sigma df estimate std.error statistic p.value
#> BackgroundX BackgroundX 1.557675 13 18.63959 0.5507212 33.84577 4.612815e-14
#> BackgroundZ BackgroundZ 1.557675 13 18.19440 0.5507212 33.03740 6.294815e-14
#> TreatmentA TreatmentA 1.557675 13 18.75377 0.5507212 34.05311 4.264271e-14
#> TreatmentB TreatmentB 1.557675 13 18.08021 0.5507212 32.83007 6.825487e-14
#> conf.low conf.high
#> BackgroundX 16.98066 20.29851
#> BackgroundZ 16.53547 19.85332
#> TreatmentA 17.09485 20.41269
#> TreatmentB 16.42129 19.73914