STAARpipeline v0.9.7

xihaoli · Feb 16, 2024 · 6a66553 · 6a66553
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diff --git a/R/noncoding.R b/R/noncoding.R
@@ -885,7 +885,7 @@ noncoding <- function(chr,gene_name,genofile,obj_nullmodel,
 	enhancervpos <- as.numeric(seqGetData(genofile,"position"))
 	enhancervref <- as.character(seqGetData(genofile,"$ref"))
 	enhancervalt <- as.character(seqGetData(genofile,"$alt"))
-	dfHancerVarGene <- data.frame(enhancervchr,enhancervpos,enhancervref,enhancervalt,enhancer2GENE)
+	dfHancerCAGEVarGene <- data.frame(enhancervchr,enhancervpos,enhancervref,enhancervalt,enhancer2GENE)
 
 	## get SNV id
 	filter <- seqGetData(genofile, QC_label)
@@ -907,18 +907,18 @@ noncoding <- function(chr,gene_name,genofile,obj_nullmodel,
 	variant.id <- seqGetData(genofile, "variant.id")
 	variant.id.SNV <- variant.id[SNVlist]
 
-	dfHancerVarGene.SNV <- dfHancerVarGene[SNVlist,]
-	dfHancerVarGene.SNV$enhancervpos <- as.character(dfHancerVarGene.SNV$enhancervpos)
-	dfHancerVarGene.SNV$enhancervref <- as.character(dfHancerVarGene.SNV$enhancervref)
-	dfHancerVarGene.SNV$enhancervalt <- as.character(dfHancerVarGene.SNV$enhancervalt)
+	dfHancerCAGEVarGene.SNV <- dfHancerCAGEVarGene[SNVlist,]
+	dfHancerCAGEVarGene.SNV$enhancervpos <- as.character(dfHancerCAGEVarGene.SNV$enhancervpos)
+	dfHancerCAGEVarGene.SNV$enhancervref <- as.character(dfHancerCAGEVarGene.SNV$enhancervref)
+	dfHancerCAGEVarGene.SNV$enhancervalt <- as.character(dfHancerCAGEVarGene.SNV$enhancervalt)
 
 	seqResetFilter(genofile)
 
-	rm(dfHancerVarGene)
+	rm(dfHancerCAGEVarGene)
 	gc()
 
 	### Gene
-	is.in <- which(dfHancerVarGene.SNV[,5]==gene_name)
+	is.in <- which(dfHancerCAGEVarGene.SNV[,5]==gene_name)
 	variant.is.in <- variant.id.SNV[is.in]
 
 	seqSetFilter(genofile,variant.id=variant.is.in,sample.id=phenotype.id)
@@ -1005,7 +1005,7 @@ noncoding <- function(chr,gene_name,genofile,obj_nullmodel,
 	results_enhancer_CAGE <- c()
 	if(inherits(pvalues, "list"))
 	{
-		results_temp <- dfHancerVarGene.SNV[1,1:4]
+		results_temp <- dfHancerCAGEVarGene.SNV[1,1:4]
 		results_temp[3] <- "enhancer_CAGE"
 		results_temp[2] <- chr
 		results_temp[1] <- as.character(gene_name)
@@ -1059,7 +1059,7 @@ noncoding <- function(chr,gene_name,genofile,obj_nullmodel,
 	enhancervpos <- as.numeric(seqGetData(genofile,"position"))
 	enhancervref <- as.character(seqGetData(genofile,"$ref"))
 	enhancervalt <- as.character(seqGetData(genofile,"$alt"))
-	dfHancerVarGene <- data.frame(enhancervchr,enhancervpos,enhancervref,enhancervalt,enhancer2GENE)
+	dfHancerrOCRsVarGene <- data.frame(enhancervchr,enhancervpos,enhancervref,enhancervalt,enhancer2GENE)
 
 	rm(varid)
 	gc()
@@ -1084,18 +1084,18 @@ noncoding <- function(chr,gene_name,genofile,obj_nullmodel,
 	variant.id <- seqGetData(genofile, "variant.id")
 	variant.id.SNV <- variant.id[SNVlist]
 
-	dfHancerVarGene.SNV <- dfHancerVarGene[SNVlist,]
-	dfHancerVarGene.SNV$enhancervpos <- as.character(dfHancerVarGene.SNV$enhancervpos)
-	dfHancerVarGene.SNV$enhancervref <- as.character(dfHancerVarGene.SNV$enhancervref)
-	dfHancerVarGene.SNV$enhancervalt <- as.character(dfHancerVarGene.SNV$enhancervalt)
+	dfHancerrOCRsVarGene.SNV <- dfHancerrOCRsVarGene[SNVlist,]
+	dfHancerrOCRsVarGene.SNV$enhancervpos <- as.character(dfHancerrOCRsVarGene.SNV$enhancervpos)
+	dfHancerrOCRsVarGene.SNV$enhancervref <- as.character(dfHancerrOCRsVarGene.SNV$enhancervref)
+	dfHancerrOCRsVarGene.SNV$enhancervalt <- as.character(dfHancerrOCRsVarGene.SNV$enhancervalt)
 
 	seqResetFilter(genofile)
 
-	rm(dfHancerVarGene)
+	rm(dfHancerrOCRsVarGene)
 	gc()
 
 	### Gene
-	is.in <- which(dfHancerVarGene.SNV[,5]==gene_name)
+	is.in <- which(dfHancerrOCRsVarGene.SNV[,5]==gene_name)
 	variant.is.in <- variant.id.SNV[is.in]
 
 	seqSetFilter(genofile,variant.id=variant.is.in,sample.id=phenotype.id)
@@ -1182,7 +1182,7 @@ noncoding <- function(chr,gene_name,genofile,obj_nullmodel,
 	results_enhancer_DHS <- c()
 	if(inherits(pvalues, "list"))
 	{
-		results_temp <- dfHancerVarGene.SNV[1,1:4]
+		results_temp <- dfHancerrOCRsVarGene.SNV[1,1:4]
 		results_temp[3] <- "enhancer_DHS"
 		results_temp[2] <- chr
 		results_temp[1] <- as.character(gene_name)
@@ -1226,8 +1226,6 @@ noncoding <- function(chr,gene_name,genofile,obj_nullmodel,
 	                          promoter_CAGE=results_promoter_CAGE,promoter_DHS=results_promoter_DHS,
 	                          enhancer_CAGE=results_enhancer_CAGE,enhancer_DHS=results_enhancer_DHS)
 
-	seqResetFilter(genofile)
-
 	return(results_noncoding)
 }
 
diff --git a/README.md b/README.md
@@ -32,7 +32,7 @@ Please see the <a href="docs/STAARpipeline_manual.pdf">**STAARpipeline** user ma
 ## 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 (February 13, 2024).
+The current version is 0.9.7 (February 16, 2024).
 ## Citation
 If you use **STAARpipeline** and **STAARpipelineSummary** for your work, please cite:
 

diff --git a/man/Gene_Centric_Coding.Rd b/man/Gene_Centric_Coding.Rd