DEqMS-style moderation for long contrast table

Splits by contrast group and applies moderated_p_deqms to each group independently.

Usage

moderated_p_deqms_long(
  mm,
  count_col,
  group_by_col = "contrast",
  estimate = "diff",
  loess_span = 0.75
)

Arguments

mm

contrast result data.frame (long format)

count_col

name of column with peptide/PSM count per protein

group_by_col

column to group by (default "contrast")

estimate

name of the fold change column

loess_span

span parameter for LOESS fit (default 0.75)

Value

data.frame with moderated columns added

See also

Other modelling: Contrasts, ContrastsFirth, ContrastsLimma, ContrastsMissing, ContrastsModerated, ContrastsModeratedDEqMS, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, ContrastsTable, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, ModelFirth, ModelLimma, build_model(), build_model_limma(), build_model_logistf(), contrasts_fisher_exact(), get_anova_df(), get_complete_model_fit(), get_p_values_pbeta(), group_label(), isSingular_lm(), linfct_all_possible_contrasts(), linfct_factors_contrasts(), linfct_from_model(), linfct_matrix_contrasts(), merge_contrasts_results(), model_analyse(), model_summary(), moderated_p_deqms(), 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_build_models_logistf(), sim_make_model_lm(), sim_make_model_lmer(), strategy_limma(), strategy_logistf(), summary_ROPECA_median_p.scaled()