TODO.md

In eriqande/gscramble: Simulating Admixed Genotypes Without Replacement

TODO

Coding stuff

• [x] in prep_gsp_for_hap_dropping() write a quick check to ensure that all the column types in the GSP tibble are correct (and that NAs are not character "NAs", etc.)
• [x] check_chrom_lengths() function (see tutorial vignette line 162)
• [x] A Function to check the validity of the GSPs.
• [x] Figure out if recombination rates between adjacent markers will work within the existing framework. (We could do that, but it would take a lot longer. We will just leave it in large bins)
• [x] Check out xover() and deal with what happens when a new breakpoint occurs exactly at an existing one, and be explicit in the documentation about whether breaks occur "to the left" or "to the right" of the breakpoint.

Functions To Document:

• [ ] big-wrapper()
• [x] check_chrom_lengths()
• [x] check_gsp_for_validity_and_saturation()
• [x] check_pedigree_for_inbreeding()
• [ ] computeQs_from_segments()
• [x] create_GSP() (just needs F1B and F1B2 params documented!)
• [ ] data() (Needs mild further description and editing for some data objects)
• [x] drop-segs-down-gsp()
• [ ] full_analysis() NOT HIGH PRIORITY. THIS IS JUST FOR VISUALIZTION
• [ ] gsp2dot()
• [ ] import()
• [ ] make_subscript_matrix()
• [ ] mat_scramble()
• [ ] perm_gs_by_pops()
• [ ] plot_simulated_chromosome_segments()
• [ ] prep_gsp_for_hap_dropping()
• [ ] rearrange_genos()
• [ ] recomb_point()
• [ ] seg2tib()
• [ ] seg_haps_through_gsp()
• [ ] segregate()
• [ ] sim_level_founder_haplos()
• [ ] tidy_up_sampled_haplos()
• [ ] xover()

In the paper

• [ ] A concise mathematical description of the components of a GSP, and the constraints between them.

For thinking

• [x] Can we come up with a framework for specifying the GSP from requests by the user for the desired end results (i.e. number of individuals of different hybrid categories.We should be able to figure this out given the constraints.

eriqande/gscramble documentation built on March 5, 2024, 4:22 p.m.