NEWS.md

In OchoaLab/polygenr: Methods for polygenic models

polygenr 0.0.0.9000 (2021-05-04)

• Initial commit, includes functions glmnet_pca, scores_glmnet, anova2, and anova_glmnet. Functions are well documented.

polygenr 0.0.1.9000 (2021-05-04)

• Functions anova2 and anova_glmnet now work when genotype matrix X has rownames with special characters. Before, for example if a locus name had the common format "chr:pos" where chr and pos are both integers, these functions would fail with this error: "Error in terms.formula(formula, data = data) : invalid model formula in ExtractVars". Now all variables are quoted with backticks, which avoids this problem. Tested to work when names have math operations such as "a+b" (treated as a single variable name now). Additionally, an informative error is thrown if a locus name actually contains a backtick (only special character we can't handle).

polygenr 0.0.2.9000 (2021-05-04)

• Function anova_glmnet now returns -log10 p-values as a sparse matrix. Pros: saves memory and runtime. Cons: had to change to return -log10 p-values instead of p-values (to retain sparsity, so that untested variants are all zero)

polygenr 0.0.3.9000 (2021-05-05)

• Function glmnet_pca how supports cross validation (a wrapper around cv.glmnet if cv = TRUE).

polygenr 0.0.4.9000 (2021-05-05)

• Added function anova_glmnet_single, for calculating scores on a single model/lambda (by default, approximately the best in terms of a precalculated cross-validation). This is in contrast to the previous function anova_glmnet, which calculates scores for all models/lambdas, which is much slower and not generally recommended anymore.

polygenr 0.0.5.9000 (2022-02-24)

• Added function anova_single for scoring a model specified by locus indexes only.
• Minor changes
• Reformatted this NEWS.md slightly to improve its automatic parsing.
• DESCRIPTION
  • Removed LazyData: true (to avoid a new "NOTE" on CRAN).
  • Added GitHub links (URL and BugReports)

OchoaLab/polygenr documentation built on March 18, 2022, 10:52 a.m.