GRaNIEdev: Added flexibilit for custom TFBS patterns, thanks to Brian for reporting

src/GRaNIEdev/R/core.R

@@ -846,13 +846,14 @@ addTFBS <- function(GRN, motifFolder, TFs = "all", nTFMax = NULL, filesTFBSPatte
   checkmate::assertDirectoryExists(motifFolder)
   checkmate::assertCharacter(TFs, min.len = 1)
   checkmate::assert(checkmate::testNull(nTFMax), checkmate::testIntegerish(nTFMax, lower = 1))
-  checkmate::assertCharacter(filesTFBSPattern, len = 1, min.chars = 1)
+  checkmate::assertCharacter(filesTFBSPattern, len = 1, min.chars = 0)
   checkmate::assertCharacter(fileEnding, len = 1, min.chars = 1)
   checkmate::assertFlag(forceRerun)
   
   if (is.null(GRN@data$TFs$translationTable) | is.null(GRN@data$TFs$translationTable) | is.null(GRN@config$allTF)  | is.null(GRN@config$directories$motifFolder) | forceRerun) {
 
-    GRN@config$TFBS_fileEnding = fileEnding
+    GRN@config$TFBS_fileEnding  = fileEnding
+    GRN@config$TFBS_filePattern = filesTFBSPattern
     GRN@data$TFs$translationTable = .getFinalListOfTFs(motifFolder, filesTFBSPattern, fileEnding, TFs, nTFMax, getCounts(GRN, type = "rna", norm = TRUE, permuted = FALSE))
     
 
@@ -868,6 +869,7 @@ addTFBS <- function(GRN, motifFolder, TFs = "all", nTFMax = NULL, filesTFBSPatte
     # GRN@config$TF_list[["all_TFBS"]] =GRN@config$allTF
     GRN@config$directories$motifFolder = motifFolder
   
+  
   } 
   
   GRN
@@ -940,6 +942,7 @@ addTFBS <- function(GRN, motifFolder, TFs = "all", nTFMax = NULL, filesTFBSPatte
     .checkAndLogWarningsAndErrors(NULL, message, isWarning = FALSE)
   }
   
+  
   HOCOMOCO_mapping.df.exp
 }
 
@@ -967,6 +970,15 @@ overlapPeaksAndTFBS <- function(GRN, nCores = 2, forceRerun = FALSE) {
 
     genomeAssembly = GRN@config$parameters$genomeAssembly
     seqlengths = .getChrLengths(genomeAssembly)
+    
+    if (!is.null(GRN@config$TFBS_filePattern)) {
+      filesTFBSPattern = GRN@config$TFBS_filePattern
+    } else {
+      message = "Could not retrieve value from GRN@config$TFBS_filePattern. Please rerun the function addTFBS, as this was added in a recent version of the package."
+      .checkAndLogWarningsAndErrors(NULL, message, isWarning = FALSE)
+    }
+   
+    
     # Check whether we have peaks on chromosomes not part of the sequence length reference. If yes, discard them
     annotation_discared = dplyr::filter(GRN@data$peaks$consensusPeaks, ! chr %in% names(seqlengths))
     
@@ -988,7 +1000,7 @@ overlapPeaksAndTFBS <- function(GRN, nCores = 2, forceRerun = FALSE) {
     res.l = .execInParallelGen(nCores, returnAsList = TRUE, listNames = GRN@config$allTF, 
                                iteration = seq_len(length(GRN@config$allTF)), 
                                verbose = FALSE, 
-                               functionName = .intersectTFBSPeaks, GRN = GRN, consensusPeaks = consensus.gr)
+                               functionName = .intersectTFBSPeaks, GRN = GRN, consensusPeaks = consensus.gr, filesTFBSPattern = filesTFBSPattern)
     
     # Sanity check
     
@@ -1028,11 +1040,11 @@ overlapPeaksAndTFBS <- function(GRN, nCores = 2, forceRerun = FALSE) {
 
 
 #' @import GenomicRanges
-.intersectTFBSPeaks <- function(GRN, TFIndex, consensusPeaks, verbose = FALSE) {
+.intersectTFBSPeaks <- function(GRN, TFIndex, consensusPeaks, filesTFBSPattern, verbose = FALSE) {
   
   TFCur = GRN@config$allTF[TFIndex]
   
-  file_tfbs_in  = paste0(GRN@config$directories$motifFolder, "/", TFCur, "_TFBS", GRN@config$TFBS_fileEnding)
+  file_tfbs_in  = paste0(GRN@config$directories$motifFolder, "/", TFCur, filesTFBSPattern, GRN@config$TFBS_fileEnding)
   
   # Intersect consensusPeaks GR with bed file GR 
   TFBS.df = .readTFBSFile(file_tfbs_in)