Package: simfam 1.1.13.9000
simfam: Simulate and Model Family Pedigrees with Structured Founders
The focus is on simulating and modeling families with founders drawn from a structured population (for example, with different ancestries or other potentially non-family relatedness), in contrast to traditional pedigree analysis that treats all founders as equally unrelated. Main function simulates a random pedigree for many generations, avoiding close relatives, pairing closest individuals according to a 1D geography and their randomly-drawn sex, and with variable children sizes to result in a target population size per generation. Auxiliary functions calculate kinship matrices, admixture matrices, and draw random genotypes across arbitrary pedigree structures starting from the corresponding founder values. The code is built around the plink FAM table format for pedigrees. There are functions that simulate independent loci and also functions that use an explicit recombination model to simulate linkage disequilibrium (LD) in the pedigree, as well as population analogs resembling the Li-Stephens model. Described in Yao and Ochoa (2023) <doi:10.7554/eLife.79238>.
Authors:
simfam_1.1.13.9000.tar.gz
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simfam.pdf |simfam.html✨
simfam/json (API)
NEWS
# Install 'simfam' in R: |
install.packages('simfam', repos = c('https://ochoalab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ochoalab/simfam/issues
- recomb_map_hg37 - Simplified recombination maps for human genomes
- recomb_map_hg38 - Simplified recombination maps for human genomes
Last updated 2 days agofrom:9ee848a8c8. Checks:OK: 9. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 19 2024 |
R-4.5-win-x86_64 | OK | Nov 19 2024 |
R-4.5-linux-x86_64 | OK | Nov 19 2024 |
R-4.4-win-x86_64 | OK | Nov 19 2024 |
R-4.4-mac-x86_64 | OK | Nov 19 2024 |
R-4.4-mac-aarch64 | OK | Nov 19 2024 |
R-4.3-win-x86_64 | OK | Nov 19 2024 |
R-4.3-mac-x86_64 | OK | Nov 19 2024 |
R-4.3-mac-aarch64 | OK | Nov 19 2024 |
Exports:admix_famadmix_last_genbim_add_posgdraw_sexfam_ancestorsgeno_famgeno_last_gengeno_last_gen_admix_recombindexes_chrkinship_famkinship_last_genpop_recombprune_famrecomb_admix_indsrecomb_famrecomb_founder_blocks_inheritedrecomb_geno_indsrecomb_haplo_indsrecomb_init_foundersrecomb_last_genrecomb_map_fix_ends_chrrecomb_map_indsrecomb_map_simplify_chrsim_pedigreetidy_recomb_map_inds
Dependencies:clidplyrfansigenericsgluelatticelifecyclemagrittrMatrixpillarpkgconfigR6Rcpprlangtibbletidyselectutf8vctrswithr