check errors
DESCRIPTION, adding missing packages, and fixed
namespaces.NEWS.md file to track changes to the
package.Overview:
s = 1 edge cases)verbose = FALSE.Additional details:
jackstraw_cluster
pool (default TRUE) to
calculate p-values by pooling null statistics (to match
jackstraw_kmeans option and default). Previously the
hardcoded behavior matched pool = FALSE.jackstraw_lfa,
jackstraw_alstructure, jackstraw_pca,
jackstraw_rpca, jackstraw_irlba,
jackstraw_subspace:
r is now second argument.
lfa, alstructure, subspace
versions: r does not have a default value and it is
mandatory.jackstraw_kmeans,
jackstraw_kmeanspp, jackstraw_MiniBatchKmeans,
jackstraw_pam, jackstraw_cluster:
s = 1 edge case: null data used to be centered
incorrectly. Bug only occurred in combination with
center = TRUE (default).RSS now returns actual
residual sum of squares. This change does not affect any exported
functions that use it. Previously RSS calculated a
normalized version (equal to 1 - R^2), but this
normalization canceled out in FSTAT (its only downstream
use), so the normalization had no user-facing effect.Exclusive list of functions without unit tests (all are redundant with other packages, so they are candidates for removal in the near future):
lfa.corpcor (redundant with lfa::lfa)pi0est_bootstrap (redundant with
qvalue::pi0est)getp (redundant with
qvalue::empPvals)devdiff_parallel (redundant with
gcatest::gcat.stat)jackstraw_pca, jackstraw_rpca,
jackstraw_irlba: Corrected documentation (parameter
r1 was incorrectly described as PC in parts of
the documentation. Thanks to Djordje Bajić (GitHub username
djbajic) for reporting this error!seed from all functions that had it. For
the same behavior, call set.seed(seed) before calling the
function.jackstraw_lfa and
jackstraw_alstructure: removed devR
option.lfa.corpcor: same as lfa::lfa with option
override = TRUEpi0est_bootstrap: redundant with
qvalue::pi0est with option
pi0.method = 'bootstrap'dev.R (internal; functionality implemented in package
gcatest)devdiff_parallel (internal; redundant with
gcatest::gcat.stat)getp (internal; redundant with
qvalue::empPvals)jackstraw_lfa now accepts genotypes input as
BEDMatrix objects. In this case, the function operates on a
low-memory mode, keeping data on disk rather than memory as much as
possible, and writes permuted data into temporary files as well. To
enable this mode, the BEDMatrix and genio
packages are now dependencies. Note only jackstraw_lfa
supports BEDMatrix because lfa supports it too
(most recent fork; see below).devdiff, which is redundant (and
replaced internally) with gcatest::delta_deviance_lf, a
function that supports more special cases, including genotypes accessed
through a BEDMatrix object. The only internal dependencies
were jackstraw_lfa and
jackstraw_alstructure.README.md to instruct users to install the most
updated forks of lfa and gcatest on GitHub
(under username alexviiia), rather than the Bioconductor
versions that are lacking critical updates.jackstraw_lfa examplejackstraw_* functions now return NA
p-values for NA statistics.
NA statistics resulted in p-values of 1 instead,
which is what qvalue::empPvals returns. Now an internal
wrapper function ensures the desired behavior.jackstraw_pam toy example unit tests that
failed often due to colinearity.NEWS.md slightly to improve its
automatic parsing.README.mdDESCRIPTIONlfa and gcatest)jackstraw_MiniBatchKmeans: internally added
suppressWarnings wrapper around
ClusterR::predict_MBatchKMeans to silence a misleading
deprecation warning. The function as a whole is not deprecated, but its
output for a case we don’t use (fuzzy=TRUE) is changing in the future.
Warning message now being suppressed:
predict_MBatchKMeans() was deprecated in
ClusterR 1.3.0.predict_MBatchKMeans will return only the
probabilities, whereas currently it also returns the hard clustersalstructure R package
(on GitHub only), user now has to provide the function to apply to data
for jackstraw_alstructure to work.NEWS.md entryREADME.mdChanges manually ported from latest CRAN branch:
VignetteBuilder: knitr since there’s no
vignette anymoreparallel which is not being
used.knitr,
rmarkdown, ggplot2, mutoss,
Matrix, gridExtra, cowplot,
scales, formatR) that were only used in a
vignette currently not being built.jackstraw_irlba and
jackstraw_rpca by 5 to keep their runtime low.jackstraw_lfa added option
permute_alleles, to change default genotype permutation to
an allele-level permutation algorithm that results in much more Binomial
data, particularly when input data is highly structured.README edited installation instructions to reflect that
dependencies lfa and gcatest are now updated
on Bioconductor (no need to install GitHub versions) and
alstructure is now optional.jackstraw_lfa changed option
permute_alleles to default to TRUE, which
performs much better, and documentation now recommends against changing
that option except for research purposes.Author and Maintainer
with Authors@R fieldjackstraw_lfa silenced warnings that occurs
only if input is BEDMatrix object and OS is Windows, in
which case some temporary files cannot be deleted during the R
session.cran-comments.mdREADME edited. Use cases as a separate subsection.DESCRIPTION edited.qvalue,
lfa, and gcatest) from Imports to Suggests, as
required by CRAN. Dependent functions will now only work if those
packages are installed:
qvalue is required for function
pip.lfa is required for functions
pseudo_Rsq and efron_Rsq, and in practice for
jackstraw_lfa too.gcatest is required for functions
jackstraw_alstructure and jackstraw_lfa.jackstraw_lfa now requires option
FUN to be defined and provided by the user (it used to
default to the lfa function)empPvals is now a copy of the
function of the same name in the qvalue package, with minor
adaptations. This is to ensure most jackstraw functions,
which depend on empPvals, work without
qvalue.m increased in unit tests to pass building in CRAN
r-devel-windows-x86_64README edited