Merge pull request #15 from stjude/p2-naming

changed output names from enhancers -> stitchedPeaks
stjude · Feb 11, 2022 · 0bdce26 · 0bdce26
2 parents 7caf426 + 117b68e
commit 0bdce26
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Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/bin/ROSE_callSuper.R b/bin/ROSE_callSuper.R
@@ -64,7 +64,7 @@ writeSuperEnhancer_table <- function(superEnhancer,description,outputFile,additi
 			warning("Additional data does not have the same number of rows as the number of super stitched peaks.\n--->>> ADDITIONAL DATA NOT INCLUDED <<<---\n")
 		}else{
 			superEnhancer <- cbind(superEnhancer,additionalData)
-			superEnhancer = superEnhancer[order(superEnhancer$enhancerRank),]
+			superEnhancer = superEnhancer[order(superEnhancer$stitchedPeakRank),]
 
 		}
 	}
@@ -128,7 +128,7 @@ cutoff_options <- calculate_cutoff(rankBy_vector, drawPlot=FALSE,xlab=paste(rank
 #These are the super-enhancers
 superEnhancerRows <- which(rankBy_vector> cutoff_options$absolute)
 typicalEnhancers = setdiff(1:nrow(stitched_regions),superEnhancerRows)
-enhancerDescription <- paste(enhancerName," Enhancers\nCreated from ", enhancerFile,"\nRanked by ",rankBy_factor,"\nUsing cutoff of ",cutoff_options$absolute," for Super-Enhancers",sep="",collapse="")
+enhancerDescription <- paste(enhancerName," Stitched Peaks\nCreated from ", enhancerFile,"\nRanked by ",rankBy_factor,"\nUsing cutoff of ",cutoff_options$absolute," for Super-Stitched Peaks",sep="",collapse="")
 
 
 #MAKING HOCKEY STICK PLOT
@@ -161,7 +161,7 @@ convert_stitched_to_bed(stitched_regions,paste(rankBy_factor,"Stitched"), enhanc
 true_super_enhancers <- stitched_regions[superEnhancerRows,]
 
 additionalTableData <- matrix(data=NA,ncol=2,nrow=nrow(stitched_regions))
-colnames(additionalTableData) <- c("enhancerRank","isSuper")
+colnames(additionalTableData) <- c("stitchedPeakRank","isSuper")
 additionalTableData[,1] <- nrow(stitched_regions)-rank(rankBy_vector,ties.method="first")+1
 additionalTableData[,2] <- 0
 additionalTableData[superEnhancerRows,2] <- 1

diff --git a/bin/ROSE_geneMapper.py b/bin/ROSE_geneMapper.py
@@ -70,7 +70,7 @@ def mapEnhancerToGene(annotFile,enhancerFile,transcribedFile='',uniqueGenes=True
     enhancerToGeneTable = [enhancerTable[5][0:6]+['OVERLAP_GENES','PROXIMAL_GENES','CLOSEST_GENE'] + enhancerTable[5][-2:]]
 
     #next by gene
-    geneToEnhancerTable = [['GENE_NAME','REFSEQ_ID','PROXIMAL_ENHANCERS']]
+    geneToEnhancerTable = [['GENE_NAME','REFSEQ_ID','PROXIMAL_STITCHED_PEAKS']]
 
 
     for line in enhancerTable[6:]:

diff --git a/bin/ROSE_main.py b/bin/ROSE_main.py
@@ -456,7 +456,7 @@ def main():
 
     time.sleep(10)
 
-    print('CALLING AND PLOTTING SUPER-ENHANCERS')
+    print('CALLING AND PLOTTING SUPER-STITCHED PEAKS')
 
 
     if options.control:
@@ -484,11 +484,11 @@ def main():
         cmd1 = "ROSE_geneMapper.py -g %s -i %s -r TRUE" % (genome,superTableFile)
         cmd2 = "ROSE_geneMapper.py -g %s -i %s -r TRUE" % (genome,allTableFile)
 
-    #gene mapper for superenhancers
+    #gene mapper for super-stitched peaks
     print(cmd1)
     os.system(cmd1)
 
-    #gene mapper for enhancers
+    #gene mapper for stitched peaks
     print(cmd2)
     os.system(cmd2)