NEWS.md

In qtl2fst: Database Storage of Genotype Probabilities for QTL Mapping

qtl2fst 0.28 (2024-07-16)

Minor changes

• Fixed link in documentation.

qtl2fst 0.26 (2021-10-07)

Minor changes

• If needed directory doesn't exist, create it rather than stopping with an error (fst_genoprob() and bind_fst() and functions that call them). Fixes Issue #17.

• Fix some URLs in Readme, News, and vignette.

• Have fst_genoprob() and genoprob_to_alleleprob_fst() check that input is of class "calc_genoprob".

qtl2fst 0.24 (2021-04-28)

Minor changes

• Fix index entry in vignette

• Added tests for qtl2::calc_het() (which previously wasn't working with qtl2fst-based probabilities). Also added tests of qtl2::calc_entropy(), qtl2::calc_geno_freq(), and qtl2::compare_genoprob(). These tests fail without qtl2 >= 0.24, so added that in Imports in the description file.

• Removed LazyData field from DESCRIPTION file

qtl2fst 0.22-7 (2020-07-24)

Minor changes

• Small changes to prepare to post on CRAN.

qtl2fst 0.22 (2020-05-26)

Major changes

• Added calc_genoprob_fst() which combines calc_genoprob() and fst_genoprob() to save use of RAM when calculating genotype probabilities.

• Added genoprob_to_alleleprob_fst() which combines genoprob_to_alleleprob() and fst_genoprob() to save use of RAM when converting genotype probabilities to allele dosages.

• Added summary() and print() functions for "fst_genoprob" objects.

• Rewrote the vignette using the iron dataset, so that it's faster to build.

Minor changes

• Fixed use of class(), avoiding constructions like "blah" %in% class(object) and instead using inherits(object, "blah").

qtl2fst 0.20 (2019-06-03)

Minor changes

• Renumbering to match R/qtl2 version

• Use Markdown for function documentation, throughout

qtl2fst 0.2-2 (2018-07-23)

Interface changes

• fst_genoprob(): added quiet argument, to replace verbose which we'll ultimately remove. Also added an argument overwrite; if FALSE (the default), refuse to overwrite the .fst files.

• Renamed fst2calc_genoprob() as fst_extract(). The function with the original name will remain for a while, but will give a warning.

• Renamed fst_genoprob_restore() as `fst_restore(). The function with the original name will remain for a while, but will give a warning.

New features

• When fst_genoprob() creates the set of .fst files with the genotype probabilities, it also creates a .rds file with the index object. Load this object with readRDS(). cbind.fst_genoprob() and rbind.fst_genoprob() will write the index .fst file for the new object.

• Added overwrite and quiet arguments to cbind.fst_genoprob() and rbind.fst_genoprob().

• Added a function fst_path() for viewing the path to the files behind an "fst_genoprob" database.

• Added a function fst_files() for viewing the set of files behind an "fst_genoprob" database.

• Added a function replace_path() for replacing the file path within a "fst_genoprob" object.

qtl2fst 0.1-3 (2018-03-13)

• New package for storing R/qtl2 genotype probabilities in files using the fst package, for fast access with reduced memory usage.

qtl2fst documentation built on Sept. 11, 2024, 5:31 p.m.