From 117b68e6f477883a80e3accf0b9fa7fa18f07c2e Mon Sep 17 00:00:00 2001 From: Adetunji Date: Thu, 10 Feb 2022 15:46:35 -0600 Subject: [PATCH] changed output names from enhancers -> stitchedPeaks --- bin/ROSE_callSuper.R | 6 +++--- bin/ROSE_geneMapper.py | 2 +- bin/ROSE_main.py | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/bin/ROSE_callSuper.R b/bin/ROSE_callSuper.R index 2e818fc..c1c98d4 100755 --- 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 index 83c6cd6..f169984 100755 --- 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 index 7e06cc0..761be5f 100755 --- 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)