Gregor Gorjanc

Sample SNP array markers with ascertainment bias by default

2

**Is your feature request related to a problem? Please describe.** Currently we selected markers for SNP array/chip at random, meaning that we can get similar distribution of allele frequencies as...

See more at https://ropensci.org/r-universe, but this is the gist > One major goal of the project is to combine live data from the build system with other sources of information,...

**Is your feature request related to a problem? Please describe.** I have now seen a couple of cases where users have been thinking that `setPheno()` will give them the same...

Write GenomicSelection vignette

1

The aim here is to show: * how to build training sets and run the models * what models and methods are implemented * Mention ascertainment bias https://github.com/gaynorr/AlphaSimR/issues/117 * Mention...

Add a bit of genomic intro to the basic vignette

7

We can pull some material from the MOOC! The idea is that we emphasise chromosomes and chromosome copies as it seems that many people don't know this well enough (even...

Convert mapping functions - providing a genetic map and implementing it with the gamma-sprinkling model * This paper describes a software that infers parameters of the gamma-sprinkling model: CODA (crossover...

We already have `setPheno()`, but there is need for more flexibility, which was the reason for fieldSim https://cran.r-project.org/src/contrib/Archive/FieldSim/ * capture GxE code/examples from Chris, Daniel&Jon, ... * capture code/examples from...

The aim is to explain how quantitative genetics is implemented in AlphaSimR Specifically: * gv, bv, dd, aa and variances https://github.com/gaynorr/AlphaSimR/issues/95 https://github.com/gaynorr/AlphaSimR/discussions/112 https://github.com/gaynorr/AlphaSimR/discussions/85 * Chris hashes out rough thought/steps *...

Lots to do here, but it would be good if someone goes through the help pages and points out sections that need more information or examples

Report realised genic variances (possibly also expected?)

3

Currently, `AlphaSimR::genParam()` returns genic variance that is in one way "realised" with respect to genotype freq and allele sub effect, but also "expected" with respect to mating, which is confusing....