getPvalues {TPP2D} | R Documentation |
Compute p-values for given F statistics based on true and null dataset
getPvalues(df_out, df_null, pseudo_count = 1, squeezeDenominator = FALSE)
df_out |
data frame containing results from analysis by fitAndEvalDataset |
df_null |
data frame containing results from analysis by bootstrapNull |
pseudo_count |
numeric larger or equal to 0 added to both counts of protein with an F-statistic higher than a threshold theta of the true and bootstrapped datasets |
squeezeDenominator |
logical indicating whether F statistic denominator should be shrinked using limma::squeezeVar |
data frame annotating each protein with a FDR based on it's F statistic and number of observations
data("simulated_cell_extract_df") temp_df <- simulated_cell_extract_df %>% filter(clustername %in% paste0("protein", 1:3)) %>% group_by(representative) %>% mutate(nObs = n()) %>% ungroup example_out <- fitAndEvalDataset(temp_df) example_null <- bootstrapNull(temp_df, B = 2) getPvalues( example_out, example_null)