support for the Asthma and Allergy array version 1.2

Author: kasperdanielhansen

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: minfi
-Version: 1.43.0
+Version: 1.43.1
 Title: Analyze Illumina Infinium DNA methylation arrays
 Description: Tools to analyze & visualize Illumina Infinium methylation arrays.
 Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("cre", "aut"),

R/read.meth.R

@@ -15,11 +15,15 @@
         arrayAnnotation <- c(
             array = "IlluminaHumanMethylationEPIC",
             annotation = .default.epic.annotation)
-    } else if (nProbes >= 54000 && nProbes <= 56000) {
+    } else if (nProbes >= 55200 && nProbes <= 55400) {
         arrayAnnotation <- c(
             array = "IlluminaHumanMethylation27k",
             annotation = .default.27k.annotation)
-    } else if (nProbes >= 41000 & nProbes <= 41100) {
+    } else if (nProbes >= 54700 && nProbes <= 54800) {
+        arrayAnnotation <- c(
+            array = "IlluminaHumanMethylationAllergy",
+            annotation = .default.allergy.annotation)
+    }  else if (nProbes >= 41000 & nProbes <= 41100) {
         arrayAnnotation <- c(
             array = "HorvathMammalMethylChip40",
             annotation = "test.unknown")

R/utils.R

@@ -7,7 +7,7 @@ utils::globalVariables(c("channel"))
 .default.27k.annotation  <- "ilmn12.hg19"
 .default.450k.annotation <- "ilmn12.hg19"
 .default.epic.annotation <- "ilm10b4.hg19"
-.default.allergy.annotation <- "ilm10.hg19"
+.default.allergy.annotation <- "ilm12.hg19"
 .metharray.types <- c("IlluminaHumanMethylation450k",
                       "IlluminaHumanMethylationEPIC",
                       "IlluminaHumanMethylation27k",

inst/NEWS.Rd

@@ -2,6 +2,13 @@
 \title{Minfi News}
 \encoding{UTF-8}
 
+\section{Version 1.43}{
+  \itemize{
+    \item {v1.43.1} Tightened the recognition code for 27k data to avoid
+    conflict with the next release of the Allergy and Asthma array.
+  }
+}
+
 \section{Version 1.39}{
   \itemize{
     \item {v1.39.1} Initial support for the Allergy and Asthma array.