Changes in version 2.1.9 (2023-07-26)
- Commented out one more strict test (NA deviances) that fail too
often on bioconductor.
Changes in version 2.1.8 (2023-07-18)
- Commented out two more strict tests (for non-negative deviances)
that fail too often on bioconductor.
Changes in version 2.1.7 (2023-06-20)
- Commented out various excessive tests against glm, which differ more
often than expected due to poor or lack of convergence.
- Removed unused LaTeX package dependencies from vignette to prevent
errors restricted to specific testing platforms.
- Fixed ..density.. deprecation warning in vignette plot.
Changes in version 2.1.6 (2023-05-25)
- Version bump for bioconductor devel.
Changes in version 2.0.6 (2023-05-25)
- README.md upgraded links from http to https
- Minor doc reformatting automatically performed by roxygen2.
Changes in version 2.0.5 (2021-06-18)
- Lots of minor changes for Bioconductor update.
- DESCRIPTION:
- Updated to Authors@R.
- Lengthened "Description" paragraph.
- Increased R dependency from 3.2 to 4.0.
- Reformatted this NEWS.md slightly to improve its automatic
parsing.
- Added examples for function delta_deviance_lf.
- Updated vignette to reflect that lfa::read.bed has been
deprecated in favor of genio::read_plink and BEDMatrix objects.
- Updated README.md, including corrections to examples.
- Updated citations:
- README.md: only had GCATest paper link, now has full
citation and also full LFA citation.
- Vignette: used to point to LFA arXiv preprint, now points to
published paper.
- inst/CITATION: didn't exist! Now includes both LFA and
GCATest papers.
- Added LICENSE.md.
- Internal changes:
- All unexported functions are now prefixed with a period.
- Replaced 1:x with seq_len(x) several functions.
- Reformatted all code with package reformatR and otherwise
match Bioconductor guidelines.
Changes in version 2.0.4.9000 (2021-05-13)
- Function delta_deviance_lf debugged case where either LF0 or LF1 is
a column matrix. Previously these 1-column matrices were getting
dropped to a vector incorrectly, which resulted in the mysterious
error message "Error: argument is of length zero". This 1-column
case is not typically observed in gcatest, but is common in the
reverse-dependent jackstraw package.
Changes in version 2.0.3.9000 (2021-05-11)
- Added function delta_deviance_lf, which calculates the delta
deviance from two logistic models and the genotype matrix data. This
function is a more general version of gcat.stat (which uses the new
function internally), to essentially consider models that differ by
more than one degree of freedom. It was written in particular for an
external application in mind, namely the jackstraw package.
- Internal function assoc_snp was renamed to delta_deviance_snp_lf and
its last argument changed to match that of delta_deviance_lf
(alternative logistic factors instead of trait).
Changes in version 2.0.2.9000 (2021-03-01)
- Added internal tests for deviance calculations against stats::glm.
- Deviance code (internal delta_deviance_snp) now returns NA instead
of stopping when an "impossible" case is encountered (when the
genotype x is non-zero but the fitted probabilities under either
null or alternative model are zero, or the alternative allele dosage
(x-2) has the same problem). These cases are clearly model fitting
failures, and can arise for common ill-defined problems,
particularly under binary adjustment variables passed to gcat
together with rare variants; these individual cases are not handled
any better by stats::glm, so it seemed most sensible to return NA at
such loci and not stop.
Changes in version 2.0.1.9000 (2021-02-16)
- Documentation updates:
- Fixed links to functions, in many cases these were broken
because of incompatible mixed Rd and markdown syntax (now
markdown is used more fully).
Changes in version 2.0.0.9000 (2020-11-13)
Major overhaul from last version (1.3.2, last updated 2016-10-06).
Visible differences are support for BEDMatrix and fewer cases in which
association p-values are NA. Internally there was major code
restructuring, and added unit tests for all functions.
- User-facing changes: Functions gcat/gcatest/gcat.stat
- added support for BEDMatrix objects for the genotype matrix X.
- This consumes lower memory when the number of loci m is very
large, so it enables analysis of larger datasets.
- Fixed some cases where the test statistic (the delta deviance)
and ultimately the p-values were NA or NaN and are no longer
missing.
- One common case is when fitted probabilities were zero or
one, which used to lead to NaN deviances when their correct
contribution was instead zero (because the limit of p*log(p)
as p goes to zero is zero, not 0 * (-Inf) = NaN).
- Other NA and NaN cases are avoided in the lfa function
af_snp (fixed in lfa 2.0.0.9000, 2020-09-18) used to
estimate the individual-specific allele frequencies used
here to compute the delta deviance. However, in rare cases
the logistic regression in af_snp fails to converge or there
are other problems, resulting in NA values propagated to
GCATest's test statistic and p-values.
- Otherwise, the new delta deviance code (function
delta_deviance_snp) is more numerically-stable than before.
- Internal changes
- Separated R functions into one source file each.
- Added more input checks to all functions.
- Added .gitignore files from another project.
- Added unit tests for all functions using testthat.
- Removed internal assoc C code
- Previously only used for genotype data without missingness
(so practically not on real datasets)
- Was entirely redundant with lfa::af_snp, which is now called
in all cases instead.
- Had bugs concerning handling of p == 0 or 1 cases that are
better handled in assoc_snp R code
- Minor scattered changes solely to pass latest R CMD check
requirements.