STAARpipelineSummary v0.9.7

xihaoli · Mar 17, 2024 · 9f9885e · 9f9885e
1 parent cf40144
commit 9f9885e
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Showing 3 changed files with 1 addition and 13 deletions.
diff --git a/R/Gene_Centric_Coding_Results_Summary.R b/R/Gene_Centric_Coding_Results_Summary.R
@@ -206,7 +206,6 @@ Gene_Centric_Coding_Results_Summary <- function(agds_dir,gene_centric_coding_job
 		disruptive_missense_sig <- results_disruptive_missense_genome[results_disruptive_missense_genome[,"STAAR-B"]<alpha,,drop=FALSE]
 		write.csv(disruptive_missense_sig,file=paste0(output_path,"disruptive_missense_sig.csv"))
 
-
 		# coding results
 		coding_sig <- rbind(plof_sig[,c("Gene name","Chr","Category","#SNV","cMAC","Burden(1,1)","STAAR-B")],
 		                    missense_sig[,c("Gene name","Chr","Category","#SNV","cMAC","Burden(1,1)","STAAR-B")])
@@ -237,7 +236,6 @@ Gene_Centric_Coding_Results_Summary <- function(agds_dir,gene_centric_coding_job
 		disruptive_missense_sig <- results_disruptive_missense_genome[results_disruptive_missense_genome[,"STAAR-O"]<alpha,,drop=FALSE]
 		write.csv(disruptive_missense_sig,file=paste0(output_path,"disruptive_missense_sig.csv"))
 
-
 		# coding results
 		coding_sig <- rbind(plof_sig[,c("Gene name","Chr","Category","#SNV","cMAC","SKAT(1,25)","Burden(1,1)","ACAT-V(1,25)","STAAR-O")],
 		                    missense_sig[,c("Gene name","Chr","Category","#SNV","cMAC","SKAT(1,25)","Burden(1,1)","ACAT-V(1,25)","STAAR-O")])
@@ -248,7 +246,6 @@ Gene_Centric_Coding_Results_Summary <- function(agds_dir,gene_centric_coding_job
 		write.csv(coding_sig,file=paste0(output_path,"coding_sig.csv"))
 	}
 
-
 	#######################################################
 	#     conditional analysis
 	#######################################################

diff --git a/R/Gene_Centric_Coding_Results_Summary_incl_ptv.R b/R/Gene_Centric_Coding_Results_Summary_incl_ptv.R
@@ -160,19 +160,16 @@ Gene_Centric_Coding_Results_Summary_incl_ptv <- function(agds_dir,gene_centric_c
 			{
 				results_synonymous_genome <- rbind(results_synonymous_genome,results)
 			}
-
 			### ptv
 			if(results[3]=="ptv")
 			{
 				results_ptv_genome <- rbind(results_ptv_genome,results)
 			}
-
 			### ptv_ds
 			if(results[3]=="ptv_ds")
 			{
 				results_ptv_ds_genome <- rbind(results_ptv_ds_genome,results)
 			}
-
 		}
 
 		if(kk%%1000==0)
@@ -213,7 +210,6 @@ Gene_Centric_Coding_Results_Summary_incl_ptv <- function(agds_dir,gene_centric_c
 	# ptv + disruptive missense
 	save(results_ptv_ds_genome,file=paste0(output_path,"ptv_ds.Rdata"))
 
-
 	if(use_SPA)
 	{
 		###### significant results

diff --git a/R/Gene_Centric_Noncoding_Results_Summary.R b/R/Gene_Centric_Noncoding_Results_Summary.R
@@ -199,7 +199,6 @@ Gene_Centric_Noncoding_Results_Summary <- function(agds_dir,gene_centric_noncodi
 	# enhancer_DHS
 	results_enhancer_DHS_genome <- results_enhancer_DHS_genome[results_enhancer_DHS_genome[,"cMAC"]>cMAC_cutoff,]
 
-
 	###### whole-genome results
 	# UTR
 	save(results_UTR_genome,file=paste0(output_path,"UTR.Rdata"))
@@ -216,16 +215,14 @@ Gene_Centric_Noncoding_Results_Summary <- function(agds_dir,gene_centric_noncodi
 	# enahncer DHS
 	save(results_enhancer_DHS_genome,file=paste0(output_path,"enhancer_DHS.Rdata"))
 
-
-	####### ncRNA
+	###### ncRNA
 	results_ncRNA_genome <- c()
 
 	for(kk in 1:ncRNA_jobs_num)
 	{
 		print(kk)
 		results_ncRNA <- get(load(paste0(ncRNA_input_path,ncRNA_results_name,"_",kk,".Rdata")))
 		results_ncRNA_genome <- rbind(results_ncRNA_genome,results_ncRNA)
-
 	}
 
 	###### cMAC_cutoff
@@ -234,7 +231,6 @@ Gene_Centric_Noncoding_Results_Summary <- function(agds_dir,gene_centric_noncodi
 	###### whole-genome results
 	save(results_ncRNA_genome,file=paste0(ncRNA_output_path,"results_ncRNA_genome.Rdata"))
 
-
 	###### significant results
 	if(!use_SPA)
 	{
@@ -340,7 +336,6 @@ Gene_Centric_Noncoding_Results_Summary <- function(agds_dir,gene_centric_noncodi
 		noncoding_sig <- rbind(noncoding_sig,ncRNA_sig)
 
 		write.csv(noncoding_sig,file=paste0(output_path,"noncoding_sig.csv"))
-
 	}
 
 	#######################################################