get_p_values_pbeta: p-value of protein from p.value of the median fold change...

In wolski/prolfqua: Proteomics Label Free Quantification

p-value of protein from p.value of the median fold change peptide.

Description

p-value of protein from p.value of the median fold change peptide.

Usage

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(), build_models(), 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(), make_model(), 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_model_and_data(), plot_lmer_peptide_noRandom(), plot_lmer_peptide_predictions(), plot_lmer_predicted_interactions(), 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)

wolski/prolfqua documentation built on May 12, 2024, 10:16 p.m.