getPvalues: Compute p-values for given F statistics based on true and...

In TPP2D: Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)

Description

Compute p-values for given F statistics based on true and null dataset

Usage

getPvalues(df_out, df_null, pseudo_count = 1, squeezeDenominator = FALSE)

Arguments

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

Value

data frame annotating each protein with a FDR based on it's F statistic and number of observations

Examples

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)
 

TPP2D documentation built on Nov. 8, 2020, 4:54 p.m.