p-value of protein from p.value of the median fold change peptide.
Source:R/tidyMS_R6_Modelling.R
get_p_values_pbeta.Rdp-value of protein from p.value of the median fold change peptide.
get_p_values_pbeta(median.p.value, n.obs, max.n = 10)Arguments
- max.n
limit number of peptides per protein.
See also
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(),
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_V1(),
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()
Examples
plot(get_p_values_pbeta(0.1,1:10,10), ylim=c(0,0.1))
plot(get_p_values_pbeta(0.1,1:10,3), ylim=c(0,0.1))
plot(get_p_values_pbeta(0.3,1:30, 3), ylim=c(0,0.1))
abline(h=.05,col = 2)
plot(seq(0.0,1.0,length=30),get_p_values_pbeta(seq(0.0,1.0,length=30),rep(10,30)))
abline(0,1)
plot(seq(0.0,1.0,length=30),get_p_values_pbeta(seq(0.0,1.0,length=30),rep(10,30),3))
abline(0,1)
testthat::expect_equal(get_p_values_pbeta(0.3,10, 3),0.216, tolerance = 1e-4)
testthat::expect_equal(get_p_values_pbeta(0,10, 3),0, tolerance = 1e-4)
testthat::expect_equal(get_p_values_pbeta(1,10, 3),1, tolerance = 1e-4)
testthat::expect_equal(get_p_values_pbeta(1,10, 3),get_p_values_pbeta(1,3, 10), tolerance = 1e-4)