STAARpipelineSummary v0.9.7

xihaoli · Jan 29, 2024 · cf40144 · cf40144
1 parent f9a4ea5
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Showing 3 changed files with 29 additions and 5 deletions.
diff --git a/R/Gene_Centric_Coding_Results_Summary.R b/R/Gene_Centric_Coding_Results_Summary.R
@@ -675,7 +675,13 @@ Gene_Centric_Coding_Results_Summary <- function(agds_dir,gene_centric_coding_job
 		colnames(genes_info_manhattan)[dim(genes_info_manhattan)[2]] <- "plof_ds"
 
 		### missense
-		results_STAAR <- results_missense_genome[,c(1,2,dim(results_missense_genome)[2]-6)]
+		if(!use_SPA)
+		{
+			results_STAAR <- results_missense_genome[,c(1,2,dim(results_missense_genome)[2]-6)]
+		}else
+		{
+			results_STAAR <- results_missense_genome[,c(1,2,dim(results_missense_genome)[2]-2)]
+		}
 
 		results_m <- c()
 		for(i in 1:dim(results_STAAR)[2])
@@ -804,7 +810,13 @@ Gene_Centric_Coding_Results_Summary <- function(agds_dir,gene_centric_coding_job
 			colnames(genes_info_manhattan)[dim(genes_info_manhattan)[2]] <- "plof_ds"
 
 			### missense
-			results_STAAR <- results_missense_genome[,c(1,2,dim(results_missense_genome)[2]-6)]
+			if(!use_SPA)
+			{
+				results_STAAR <- results_missense_genome[,c(1,2,dim(results_missense_genome)[2]-6)]
+			}else
+			{
+				results_STAAR <- results_missense_genome[,c(1,2,dim(results_missense_genome)[2]-2)]
+			}
 
 			results_m <- c()
 			for(i in 1:dim(results_STAAR)[2])

diff --git a/R/Gene_Centric_Coding_Results_Summary_incl_ptv.R b/R/Gene_Centric_Coding_Results_Summary_incl_ptv.R
@@ -869,7 +869,13 @@ Gene_Centric_Coding_Results_Summary_incl_ptv <- function(agds_dir,gene_centric_c
 		colnames(genes_info_manhattan)[dim(genes_info_manhattan)[2]] <- "plof_ds"
 
 		### missense
-		results_STAAR <- results_missense_genome[,c(1,2,dim(results_missense_genome)[2]-6)]
+		if(!use_SPA)
+		{
+			results_STAAR <- results_missense_genome[,c(1,2,dim(results_missense_genome)[2]-6)]
+		}else
+		{
+			results_STAAR <- results_missense_genome[,c(1,2,dim(results_missense_genome)[2]-2)]
+		}
 
 		results_m <- c()
 		for(i in 1:dim(results_STAAR)[2])
@@ -1045,7 +1051,13 @@ Gene_Centric_Coding_Results_Summary_incl_ptv <- function(agds_dir,gene_centric_c
 			colnames(genes_info_manhattan)[dim(genes_info_manhattan)[2]] <- "plof_ds"
 
 			### missense
-			results_STAAR <- results_missense_genome[,c(1,2,dim(results_missense_genome)[2]-6)]
+			if(!use_SPA)
+			{
+				results_STAAR <- results_missense_genome[,c(1,2,dim(results_missense_genome)[2]-6)]
+			}else
+			{
+				results_STAAR <- results_missense_genome[,c(1,2,dim(results_missense_genome)[2]-2)]
+			}
 
 			results_m <- c()
 			for(i in 1:dim(results_STAAR)[2])

diff --git a/README.md b/README.md
@@ -31,7 +31,7 @@ Please see the <a href="docs/STAARpipelineSummary_manual.pdf">**STAARpipelineSum
 ## Data Availability
 The whole-genome functional annotation data assembled from a variety of sources and the precomputed annotation principal components are available at the [Functional Annotation of Variant - Online Resource (FAVOR)](https://favor.genohub.org) site and [FAVOR Essential Database](https://doi.org/10.7910/DVN/1VGTJI).
 ## Version
-The current version is 0.9.7 (November 11, 2023).
+The current version is 0.9.7 (January 29, 2024).
 ## Citation
 If you use **STAARpipeline** and **STAARpipelineSummary** for your work, please cite: