@@ -1,7 +1,7 @@

 Package: TPP2D

 Title: Detection of ligand-protein interactions from 2D thermal 

     profiles (DLPTP)

-Version: 1.3.13

+Version: 1.3.14

 Authors@R: c(

     person("Nils", "Kurzawa", email = "nils.kurzawa@embl.de", 

         role = c("aut", "cre")),

@@ -23,5 +23,5 @@ URL: http://bioconductor.org/packages/TPP2D

 RoxygenNote: 6.1.1

 Depends: R (>= 3.6.0), stats, utils, dplyr, methods

 Imports: ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, 

-  RCurl, parallel, MASS, BiocParallel

+  RCurl, parallel, MASS, BiocParallel, limma

 Suggests: knitr, testthat

@@ -37,6 +37,7 @@ importFrom(RCurl,url.exists)

 importFrom(doParallel,registerDoParallel)

 importFrom(foreach,"%dopar%")

 importFrom(foreach,foreach)

+importFrom(limma,squeezeVar)

 importFrom(methods,is)

 importFrom(methods,new)

 importFrom(openxlsx,read.xlsx)

@@ -5,6 +5,8 @@

 #' fitAndEvalDataset

 #' @param df_null data frame containing results from analysis by

 #' bootstrapNull

+#' @param squeezeDenominator logical indicating whether F statistic

+#' denominator should be shrinked using limma::squeezeVar

 #' 

 #' @return data frame annotating each protein with a FDR based on 

 #' it's F statistic and number of observations

@@ -23,12 +25,17 @@

 #' @export

 #'

 #' @import dplyr

-getFDR <- function(df_out, df_null){

+getFDR <- function(df_out, df_null, squeezeDenominator = TRUE){

     dataset <- nObs <- nObsRound <- F_statistic <- 

         is_decoy <- max_rank <- true_cumsum <- 

         null_cumsum <- representative <- clustername <- 

         dataset <- FDR <- all_true <- all_null <- NULL

+    if(squeezeDenominator){

+        df_out <- .shrinkFstat(df_out, trueOrNull = "true")

+        df_null <- .shrinkFstat(df_null, trueOrNull = "null")

+    }

+    

     B <- max(as.numeric(

         gsub("bootstrap_", "", unique(df_null$dataset))))

@@ -52,6 +59,31 @@ getFDR <- function(df_out, df_null){

     return(out_df)

 }

+#' @importFrom limma squeezeVar 

+.shrinkFstat <- function(inDf, trueOrNull = "true"){

+    rssH1 <- df2 <- rssH0 <- rssH1Squeezed <- df1 <- 

+        nObs <- nObsRound <- dataset <- NULL

+    if(trueOrNull == "true"){

+        outDf <- inDf %>% 

+            mutate(nObsRound = round(nObs/10)*10) %>% 

+            group_by(nObsRound) %>% 

+            mutate(rssH1Squeezed = limma::squeezeVar(

+                rssH1, df = df2)$var.post) %>% 

+            ungroup %>% 

+            mutate(F_statistic = (rssH0 - rssH1)/

+                       (rssH1Squeezed) * df2/df1)

+    }else if(trueOrNull == "null"){

+        outDf <- inDf %>% 

+            mutate(nObsRound = round(nObs/10)*10) %>% 

+            group_by(dataset, nObsRound) %>% 

+            mutate(rssH1Squeezed = limma::squeezeVar(

+                rssH1, df = df2)$var.post) %>% 

+            ungroup %>% 

+            mutate(F_statistic = (rssH0 - rssH1)/

+                       (rssH1Squeezed) * df2/df1)

+    }

+    return(outDf)

+}

 #' Compute FDR for given F statistics based on true and

 #' null dataset (old function)

 #' 

@@ -5,7 +5,7 @@

 \title{Get FDR for given F statistics based on true and

 null dataset}

 \usage{

-getFDR(df_out, df_null)

+getFDR(df_out, df_null, squeezeDenominator = TRUE)

 }

 \arguments{

 \item{df_out}{data frame containing results from analysis by

@@ -13,6 +13,9 @@ fitAndEvalDataset}

 \item{df_null}{data frame containing results from analysis by

 bootstrapNull}

+

+\item{squeezeDenominator}{logical indicating whether F statistic

+denominator should be shrinked using limma::squeezeVar}

 }

 \value{

 data frame annotating each protein with a FDR based on 

@@ -7,4 +7,4 @@ test_that("computeFStatFromParams works as expected", {

                                       filter(representative %in% 1:3))

     fstat_df <- computeFStatFromParams(params_df)

     expect_equal(round(fstat_df$F_statistic, 2), c(1.23, 0.36, 0.24), tolerance = 0.015)

-})

\ No newline at end of file

+})