simtrait 1.0.0.9000 (2019-02-13)

simtrait 1.0.1.9000 (2019-03-26)

Renamed argument sigmaSq to sigma_sq (parameter of sim_trait and cov_trait).
sim_trait return list has more descriptive names:
- trait (old y)
- causal_indexes (old i)
- causal_coeffs (old beta)
Overall coding style changes.
Vignette changes in parallel with popkin 1.2.0.9000 changes.

Added allele_freqs, which handles BEDMatrix objects correctly. Rest of sim_trait doesn’t handle BEDMatrix objects yet.

Now sim_trait, and consequently the whole package, supports BEDMatrix objects. This is ideal for simulating traits from real and potentially very large genotype data.

Improved allele_freqs to load genotype chunks from a BEDMatrix object more efficiently, using as much available memory as possible. Requires an updated popkin package (>= 1.2.6.9000).

Preemptively updated class usage now that matrices return a two-element array in R-devel
Moved logo to man/figures/
Minor Roxygen-related updates

Function sim_trait changed default maf_cut from 0.05 to NA, and in that case code no longer computes marginal allele frequencies unless they are needed because p_anc is missing (and kinship is provided). This is much faster and memory efficient in extremely large simulations, and just makes more sense to me generally (the MAF threshold was a quirky feature, still available but non-default now).

Function sim_trait now delays calculating allele frequencies if maf_cut = NA and p_anc is missing (and kinship is provided), so that these frequencies are only calculated on the small subset of loci selected to be causal (rather than the whole genome, which was the original behavior). This is expected to speed-up trait simulations from real genotypes.
Vignette had minor corrections and edits (focused on model and algorithm description).

Added function sim_trait_mvn, which draws traits from the multivariate normal distribution with covariance structure matching that of genetic traits (also called “infinitesimal” model). These traits are useful for testing heritability estimation. A visual validation of these simulated traits is available in the vignette.

Function alelle_freq was modified to reduce memory usage for the BEDMatrix case.
- For both this function and sim_trait, the BEDMatrix-specific options mem_factor and mem_lim were replaced by the option m_chunk_max.
- As a consequence of the changes, popkin is no longer a dependency of this simtrait package. However, popkin is still recommended for estimating the kinship matrices required by some of the functions of this simtrait package.

Added functions used for benchmarking genetic association methods based on traits simulated with simtrait:
- rmsd: General root-mean-square deviation (RMSD) function
- pval_srmsd: Signed RMSD between observed and expected (uniform) p-values
- pval_aucpr: Area under the curve (AUC) of precision-recall (PR) curve
  - Added PRROC package dependency

Added function pval_infl (classic inflation factor, but from p-values) to complement yesterday’s new functions

Function allele_freqs added option fold, which if TRUE returns folded i.e. minor allele frequencies. Default is FALSE, to return allele frequencies for the alternative allele (the allele counted as it given in the genotype matrix, whether it is the minor or major allele).

Function sim_trait added option const_herit_loci, which when TRUE constructs causal coefficients as inversely proportional to the square root of p*(1-p), where p is the ancestral allele frequency. This ensures equal per-causal-locus contribution to trait variance. Default draws causal coefficients randomly from a standard normal distribution, rescaled to result in the desired heritability, for unequal per-locus contribution to trait variance.
Added function herit_loci, which calculates per-locus heritabilities based on variance formula (in terms of allele frequencies, coefficients, and overall trait variance factor).
- Used to validate function sim_trait in unit tests.

Function sim_trait with option const_herit_loci = TRUE now adds random signs (+/-) to the causal coefficients.
- Added usage example for this option to vignette.

Function sim_trait now requires that p_anc have the same length as the number of loci in X (stops with an error otherwise). Previously this was not checked and could return traits that were NA for all individuals without clear indications that anything was wrong.

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).

Function pval_srmsd now accepts causal_indexes = NULL to handle cases where all p-values are null (before a NULL input would cause an error).

First CRAN submission!
Major changes
- Function sim_trait renamed option const_herit_loci to fes (fixed effect sizes), the language used in the paper.
- Updated documentation generally to agree with paper and to be more concise.
  - “betas” are exclusively referred to as regression coefficients (used to be referred to incorrectly as effect sizes)
  - Package-wide doc now includes all key functions in examples.
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)
- Fixed spelling in documentation.