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 = TRUE
pi0est_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_*
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.jackstraw_alstructure
because dependency alstructure
is not on CRAN or Bioconductor.jackstraw_lfa
because the latest versions of the dependencies lfa
and gcatest
on Bioconductor do not support BEDMatrix (the development versions that do support BEDMatrix are on GitHub only).lfa
and gcatest
devel version requirements.delta_deviance_lf
, delta_deviance_snp
, delta_deviance_snp_lf
, which are copies of the gcatest
functions of the same name (available on development version only, hence this copying)VignetteBuilder: knitr
since there’s no vignette anymorejackstraw_lfa
and package dependencies lfa
and gcatest
, since lfa
is having build errors on bioc-devel.
pseudo_Rsq
, mcfadden_Rsq_snp
, efron_Rsq
, efron_Rsq_snp
, delta_deviance_{lf,snp,snp_lf}.R
(all depended on lfa
)parallel
and genio
which are temporarily 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.