update hlaUniqueAllele()

zhengxwen · May 8, 2024 · 5cc9d16 · 5cc9d16
1 parent 711acec
commit 5cc9d16
Showing 3 changed files with 15 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: HIBAG
 Type: Package
 Title: HLA Genotype Imputation with Attribute Bagging
-Version: 1.39.5
-Date: 2024-04-11
+Version: 1.40.1
+Date: 2024-05-07
 Depends: R (>= 3.2.0)
 Imports: methods, RcppParallel
 Suggests: parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray, knitr,

diff --git a/NEWS b/NEWS
@@ -1,3 +1,13 @@
+CHANGES IN VERSION 1.41.1
+-------------------------
+
+    o the input of `hlaUniqueAllele()` can be a hlaAttrBagClass object or
+      a hlaAttrBagObj object
+
+    o `hlaAlleleToVCF()` outputs 0 instead of NaN if the location of HLA gene
+      is unknown or unspecified
+
+
 CHANGES IN VERSION 1.40.0
 -------------------------
 

diff --git a/man/hlaUniqueAllele.Rd b/man/hlaUniqueAllele.Rd
@@ -10,8 +10,9 @@
 hlaUniqueAllele(hla, all=NA)
 }
 \arguments{
-    \item{hla}{character-type HLA alleles, or a \code{\link{hlaAlleleClass}}
-        object}
+    \item{hla}{character-type HLA alleles, a \code{\link{hlaAlleleClass}}
+        object, a \code{link{hlaAttrBagClass}} object, or
+        a \code{link{hlaAttrBagObj}} object}
     \item{all}{when \code{hla} is a \code{hlaAlleleClass} object and
         \code{all=TRUE}, return all HLA alleles if \code{hla$dosage} or
         \code{hla$postprob} exists; otherwise, only return the alleles in