diff --git a/DESCRIPTION b/DESCRIPTION index 4f0b3bf..4b1e356 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: HIBAG Type: Package Title: HLA Genotype Imputation with Attribute Bagging -Version: 1.38.2 -Date: 2024-01-19 +Version: 1.38.3 +Date: 2024-01-29 Depends: R (>= 3.2.0) Imports: methods, RcppParallel Suggests: parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray, knitr, diff --git a/NEWS b/NEWS index 4cb33e4..378cbc4 100644 --- a/NEWS +++ b/NEWS @@ -1,4 +1,4 @@ -CHANGES IN VERSION 1.38.2 +CHANGES IN VERSION 1.38.3 ------------------------- o fix compiler warnings: -Wformat & -Wformat-security @@ -6,6 +6,8 @@ CHANGES IN VERSION 1.38.2 o new 'use.matching=TRUE' in `hlaPredMerge()`; to set 'use.matching=FALSE' for backward compatibility + o 'ret.postprob=FALSE' by default in `hlaPredMerge()` + CHANGES IN VERSION 1.38.1 ------------------------- diff --git a/R/HIBAG.R b/R/HIBAG.R index d41ae0e..c90b97e 100644 --- a/R/HIBAG.R +++ b/R/HIBAG.R @@ -5,7 +5,7 @@ # HIBAG -- HLA Genotype Imputation with Attribute Bagging # # HIBAG R package, HLA Genotype Imputation with Attribute Bagging -# Copyright (C) 2011-2022 Xiuwen Zheng (zhengx@u.washington.edu) +# Copyright (C) 2011-2024 Xiuwen Zheng (zhengx@u.washington.edu) # All rights reserved. # # This program is free software: you can redistribute it and/or modify @@ -823,7 +823,7 @@ hlaPredict <- function(object, snp, cl=FALSE, # hlaPredMerge <- function(..., weight=NULL, equivalence=NULL, use.matching=TRUE, - ret.dosage=TRUE, ret.postprob=TRUE, max.resolution="", rm.suffix=FALSE) + ret.dosage=TRUE, ret.postprob=FALSE, max.resolution="", rm.suffix=FALSE) { # check "..." pdlist <- list(...) diff --git a/README.md b/README.md index 46c7c4a..2122fdf 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ HIBAG is a state of the art software package for imputing HLA types using SNP da ## Bioconductor Package -Release Version: 1.38.0 +Release Version: 1.38.3 [http://www.bioconductor.org/packages/HIBAG/](http://www.bioconductor.org/packages/HIBAG/) diff --git a/man/hlaPredMerge.Rd b/man/hlaPredMerge.Rd index 7460201..136cd8b 100644 --- a/man/hlaPredMerge.Rd +++ b/man/hlaPredMerge.Rd @@ -9,7 +9,7 @@ HLA types. } \usage{ hlaPredMerge(..., weight=NULL, equivalence=NULL, use.matching=TRUE, - ret.dosage=TRUE, ret.postprob=TRUE, max.resolution="", rm.suffix=FALSE) + ret.dosage=TRUE, ret.postprob=FALSE, max.resolution="", rm.suffix=FALSE) } \arguments{ \item{...}{The object(s) of \code{\link{hlaAlleleClass}}, having a field