Fix get.annotation function for EPIC v2 / Clean code

epigen · Oct 5, 2023 · 572359f · 572359f
1 parent ae92403
commit 572359f
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Showing 4 changed files with 3 additions and 5 deletions.
diff --git a/R/RnBeadRawSet-class.R b/R/RnBeadRawSet-class.R
@@ -265,7 +265,6 @@ RnBeadRawSet<-function(
 		}
 
 
-		saveRDS(probes, "/Users/baris.kalem/Code/RnBeads/probes.RDS")
 		res<-match.probes2annotation(probes, target, assembly)
 		sites<-res[[1]]
 		site.ids<-res[[2]]

diff --git a/R/annotations.R b/R/annotations.R
@@ -766,8 +766,7 @@ rnb.get.assemblies <- function() {
 #' \donttest{
 #' rnb.get.annotation("promoters")
 #' }
-rnb.get.annotation <- function(type = "CpG", assembly = "hg38") {
-	## TODO: Make it hg38 compatible
+rnb.get.annotation <- function(type = "CpG", assembly = "hg19") {
 	if (!(is.character(type) && length(type) == 1 && (!is.na(type)))) {
 		stop("invalid value for type")
 	}

diff --git a/R/controlPlots.R b/R/controlPlots.R
@@ -60,7 +60,7 @@ rnb.plot.control.boxplot <- function(
 	if(rnb.set@target=="probesEPIC"){
 		meta <- rnb.get.annotation("controlsEPIC")
 	}else if(rnb.set@target=="probesEPICv2"){
-		meta <- rnb.get.annotation("controlsEPICv2")
+		meta <- rnb.get.annotation("controlsEPICv2", assembly = "hg38")
 	}else if(rnb.set@target=="probes450"){
 		meta <- rnb.get.annotation("controls450")
 	}else if(rnb.set@target=="probes27"){

diff --git a/R/qualityControl.R b/R/qualityControl.R
@@ -392,7 +392,7 @@ add.qc.barplots<-function(report, object, sample.batch.size=50){
 	  cmd <- rnb.get.annotation("controlsEPIC")
 	  ctypes<-unique(cmd$Target)[unique(cmd$Target) %in% rnb.infinium.control.targets("probesEPIC")[c(14,4,3,15,1:2,12:13,6,11)]]
   }else if(object@target=="probesEPICv2"){
-	  cmd <- rnb.get.annotation("controlsEPICv2")
+	  cmd <- rnb.get.annotation("controlsEPICv2", assembly = "hg38")
 	  ctypes<-unique(cmd$Target)[unique(cmd$Target) %in% rnb.infinium.control.targets("probesEPICv2")[c(14,4,3,15,1:2,12:13,6,11)]]
   }else if(object@target=="probes450"){
   	cmd <- rnb.get.annotation("controls450")