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".
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
Added calc_genoprob_fst() which combines
calc_genoprob() and fst_genoprob() to save use
of RAM when calculating genotype probabilties.
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.
Added summary() and print() functions
for "fst_genoprob" objects.
Rewrote the vignette using the iron dataset, so that it’s faster to build.
class(), avoiding constructions like
"blah" %in% class(object) and instead using
inherits(object, "blah").Renumbering to match R/qtl2 version
Use Markdown for function documentation, throughout
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.
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.