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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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.