ContrastsFirth: Estimate contrasts using Wald Test

In wolski/prolfqua: Proteomics Label Free Quantification

Estimate contrasts using Wald Test

Description

Estimate contrasts using Wald Test

Estimate contrasts using Wald Test

Super class

prolfqua::ContrastsInterface -> ContrastFrith

Public fields

models

Model

contrasts

character with contrasts

contrastfun

function to compute contrasts

subject_Id

name of column containing e.g., protein Id's

p.adjust

function to adjust p-values (default prolfqua::adjust_p_values)

contrast_result

data frame containing results of contrast computation

Active bindings

contrastfun

function to compute contrasts

Methods

Public methods

• ContrastsFirth$new()

• ContrastsFirth$get_contrast_sides()

• ContrastsFirth$get_linfct()

• ContrastsFirth$get_contrasts()

• ContrastsFirth$get_Plotter()

• ContrastsFirth$to_wide()

• ContrastsFirth$clone()

Inherited methods

• prolfqua::ContrastsInterface$column_description()

---

Method new()

initialize create Contrast

Usage

ContrastsFirth$new(
  model,
  contrasts,
  p.adjust = prolfqua::adjust_p_values,
  modelName = "WaldTestFirth"
)

Arguments

model

a dataframe with a structure similar to that generated by build_model

contrasts

a character vector with contrast specificiation

p.adjust

function to adjust the p-values

modelName

name of contrast method, default WaldTest

---

Method get_contrast_sides()

get both sides of contrasts

Usage

ContrastsFirth$get_contrast_sides()

---

Method get_linfct()

get linear functions from contrasts

Usage

ContrastsFirth$get_linfct(avg = TRUE)

Arguments

avg

logical TRUE - get also linfct for averages

---

Method get_contrasts()

get table with contrast estimates

Usage

ContrastsFirth$get_contrasts(all = FALSE)

Arguments

all

should all columns be returned (default FALSE)

Returns

data.frame with contrasts

---

Method get_Plotter()

return ContrastsPlotter creates Contrast_Plotter

Usage

ContrastsFirth$get_Plotter(FCthreshold = 1, FDRthreshold = 0.1)

Arguments

FCthreshold

fold change threshold to show in plots

FDRthreshold

FDR threshold to show in plots

Returns

ContrastsPlotter

---

Method to_wide()

convert to wide format

Usage

ContrastsFirth$to_wide(columns = c("p.value", "FDR", "statistic"))

Arguments

columns

value column default p.value

Returns

data.frame

---

Method clone()

The objects of this class are cloneable with this method.

Usage

ContrastsFirth$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

See Also

Other modelling: Contrasts, ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, ContrastsTable, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, ModelFirth, build_model(), build_model_logistf(), 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

modi <- sim_build_models_logistf(model = "parallel3", weight_missing = 1)
contrasts <- c(Avs = "group_A - group_B", AvsCtrl = "group_A - group_Ctrl")

ctr <- ContrastsFirth$new(modi,contrasts)
ctr$get_contrast_sides()
ctr$get_linfct()
ctr$get_contrasts()

mod3 <- sim_build_models_logistf(model = "parallel3", weight_missing = 1, peptide=TRUE)

# ContrastsFirth$debug("get_contrasts")
ctrpep <- ContrastsFirth$new(mod3,contrasts)
ctrpep$get_contrast_sides()

ctrpep$get_linfct()
ctrpep$get_contrasts()
pl <- ctrpep$get_Plotter()

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