NEWS.md

In StoreyLab/gcatest: Genotype Conditional Association TEST

gcatest 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.

gcatest 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).

gcatest 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.

gcatest 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).

gcatest 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.

gcatest 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.

gcatest 2.0.6 (2023-05-25)

• README.md upgraded links from http to https
• Minor doc reformatting automatically performed by roxygen2.

gcatest 2.1.6 (2023-05-25)

• Version bump for bioconductor devel.

gcatest 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.

gcatest 2.1.8 (2023-07-18)

• Commented out two more strict tests (for non-negative deviances) that fail too often on bioconductor.

gcatest 2.1.9 (2023-07-26)

• Commented out one more strict test (NA deviances) that fail too often on bioconductor.

StoreyLab/gcatest documentation built on March 7, 2024, 9:59 p.m.