diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index a3ac618..447b6fb 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -2,9 +2,9 @@ # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: [main, master] + branches: [main, master, cran] pull_request: - branches: [main, master] + branches: [main, master, cran] name: R-CMD-check diff --git a/DESCRIPTION b/DESCRIPTION index 5f678fb..11406b2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: qtl2fst -Version: 0.26 -Date: 2021-10-07 +Version: 0.28 +Date: 2024-07-16 Title: Database Storage of Genotype Probabilities for QTL Mapping Description: Uses the 'fst' package to store genotype probabilities on disk for the 'qtl2' package. These genotype probabilities are a central data object for mapping quantitative trait loci (QTL), but they can be quite large. The facilities in this package enable the genotype probabilities to be stored on disk, leading to reduced memory usage with only a modest increase in computation time. Author: Karl W Broman [aut, cre] (), @@ -26,5 +26,5 @@ License: GPL-3 URL: https://github.com/rqtl/qtl2fst ByteCompile: true Encoding: UTF-8 -RoxygenNote: 7.1.2 +RoxygenNote: 7.3.2 Roxygen: list(markdown=TRUE) diff --git a/NEWS.md b/NEWS.md index 12fd9b4..5de70bf 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +## qtl2fst 0.28 (2024-07-16) + +### Minor changes + +- Fixed link in documentation. + + ## qtl2fst 0.26 (2021-10-07) ### Minor changes @@ -40,11 +47,11 @@ - Added `calc_genoprob_fst()` which combines `calc_genoprob()` and `fst_genoprob()` to save use of RAM when calculating genotype - probabilties. + probabilities. - Added `genoprob_to_alleleprob_fst()` which combines `genoprob_to_alleleprob()` and `fst_genoprob()` to save use of RAM - when converting genotype probabilties to allele dosages. + when converting genotype probabilities to allele dosages. - Added `summary()` and `print()` functions for `"fst_genoprob"` objects. diff --git a/R/genoprob_to_alleleprob_fst.R b/R/genoprob_to_alleleprob_fst.R index 6382efe..36428bf 100644 --- a/R/genoprob_to_alleleprob_fst.R +++ b/R/genoprob_to_alleleprob_fst.R @@ -2,10 +2,10 @@ #' Convert genotype probabilities to allele probabilities and write to fst database #' #' Reduce genotype probabilities (as calculated by -#' [calc_genoprob()]) to allele probabilities, writing them to an fst database. +#' [qtl2::calc_genoprob()]) to allele probabilities, writing them to an fst database. #' #' @param probs Genotype probabilities, as calculated from -#' [calc_genoprob()]. +#' [qtl2::calc_genoprob()]. #' @param fbase Base of filename for fst database. #' @param fdir Directory for fst database. #' @param quiet IF `FALSE`, print progress messages. diff --git a/man/genoprob_to_alleleprob_fst.Rd b/man/genoprob_to_alleleprob_fst.Rd index 44a6117..df35775 100644 --- a/man/genoprob_to_alleleprob_fst.Rd +++ b/man/genoprob_to_alleleprob_fst.Rd @@ -16,7 +16,7 @@ genoprob_to_alleleprob_fst( } \arguments{ \item{probs}{Genotype probabilities, as calculated from -\code{\link[=calc_genoprob]{calc_genoprob()}}.} +\code{\link[qtl2:calc_genoprob]{qtl2::calc_genoprob()}}.} \item{fbase}{Base of filename for fst database.} @@ -39,7 +39,7 @@ collapsed to alleles rather than genotypes. } \description{ Reduce genotype probabilities (as calculated by -\code{\link[=calc_genoprob]{calc_genoprob()}}) to allele probabilities, writing them to an fst database. +\code{\link[qtl2:calc_genoprob]{qtl2::calc_genoprob()}}) to allele probabilities, writing them to an fst database. } \details{ This is like calling \code{qtl2::genoprob_to_alleleprob()} and then