getPvalues {TPP2D} | R Documentation

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

### 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)

[Package TPP2D version 1.10.0 Index]