From 5f6653242cd59885df064e9cc502b01bbd85936c Mon Sep 17 00:00:00 2001
From: Xiuwen Zheng <zhengxwen@users.noreply.github.com>
Date: Thu, 14 Mar 2024 20:44:12 -0500
Subject: [PATCH] new option 'all' in hlaUniqueAllele()
---
DESCRIPTION | 4 ++--
NEWS | 6 ++++++
R/DataUtilities.R | 16 ++++++++++++++--
man/hlaUniqueAllele.Rd | 10 +++++++---
4 files changed, 29 insertions(+), 7 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index a399433..4a611ed 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: HIBAG
Type: Package
Title: HLA Genotype Imputation with Attribute Bagging
-Version: 1.38.4
-Date: 2024-03-11
+Version: 1.39.4
+Date: 2024-03-14
Depends: R (>= 3.2.0)
Imports: methods, RcppParallel
Suggests: parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray, knitr,
diff --git a/NEWS b/NEWS
index 378cbc4..2d7d37d 100644
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,9 @@
+CHANGES IN VERSION 1.39.4
+-------------------------
+
+ o new option 'all' in `hlaUniqueAllele()`
+
+
CHANGES IN VERSION 1.38.3
-------------------------
diff --git a/R/DataUtilities.R b/R/DataUtilities.R
index 75ad5a4..4324d48 100644
--- a/R/DataUtilities.R
+++ b/R/DataUtilities.R
@@ -1136,7 +1136,7 @@ hlaAlleleDigit <- function(obj, max.resolution=NA_character_, rm.suffix=FALSE)
# Get unique HLA alleles
#
-hlaUniqueAllele <- function(hla)
+hlaUniqueAllele <- function(hla, all=NA)
{
# check
stopifnot(is.character(hla) | inherits(hla, "hlaAlleleClass"))
@@ -1147,7 +1147,19 @@ hlaUniqueAllele <- function(hla)
hla <- unique(hla)
.Call(HIBAG_SortAlleleStr, hla)
} else {
- hlaUniqueAllele(as.character(c(hla$value$allele1, hla$value$allele2)))
+ s <- c(hla$value$allele1, hla$value$allele2)
+ if (isTRUE(all))
+ {
+ if (!is.null(hla$dosage))
+ {
+ s <- rownames(hla$dosage)
+ } else if (!is.null(hla$postprob))
+ {
+ s <- strsplit(rownames(hla$postprob), "/", fixed=TRUE)
+ s <- unique(unlist(s))
+ }
+ }
+ hlaUniqueAllele(as.character(s))
}
}
diff --git a/man/hlaUniqueAllele.Rd b/man/hlaUniqueAllele.Rd
index 52487f7..ad050a9 100644
--- a/man/hlaUniqueAllele.Rd
+++ b/man/hlaUniqueAllele.Rd
@@ -7,11 +7,15 @@
Get unique HLA alleles, which are in ascending order.
}
\usage{
-hlaUniqueAllele(hla)
+hlaUniqueAllele(hla, all=NA)
}
\arguments{
- \item{hla}{character-type HLA alleles, or a
- \code{\link{hlaAlleleClass}} object}
+ \item{hla}{character-type HLA alleles, or a \code{\link{hlaAlleleClass}}
+ 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
+ \code{hla$value}}
}
\details{
Each HLA allele name has a unique number corresponding to up to four sets