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simfam
View on CRAN: Click
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Download and install simfam package within the R console
Install from CRAN:
install.packages("simfam")
Install from Github:
library("remotes")
install_github("cran/simfam")
Install by package version:
library("remotes")
install_version("simfam", "1.1.6")
Attach the package and use:
library("simfam")
Maintained by
Alejandro Ochoa
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-09-02
Latest Update: 2023-01-09
Description:
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.Described in Yao and Ochoa (2022) <doi:10.1101/2022.03.25.485885>.
How to cite:
Alejandro Ochoa (2021). simfam: Simulate and Model Family Pedigrees with Structured Founders. R package version 1.1.6, https://cran.r-project.org/web/packages/simfam. Accessed 21 Nov. 2024.
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Complete documentation for simfam
Functions, R codes and Examples using
the simfam R package
Some associated functions: admix_fam . admix_last_gen . draw_sex . fam_ancestors . geno_fam . geno_last_gen . kinship_fam . kinship_last_gen . prune_fam . recomb_admix_inds . recomb_fam . recomb_geno_inds . recomb_haplo_inds . recomb_init_founders . recomb_last_gen . recomb_map_fix_ends_chr . recomb_map_hg . recomb_map_inds . recomb_map_simplify_chr . sim_pedigree . simfam-package .
Some associated R codes: RcppExports.R . admix_fam.R . admix_last_gen.R . data.R . draw_couples_nearest.R . draw_num_children_per_fam.R . draw_sex.R . fam_ancestors.R . geno_fam.R . geno_last_gen.R . kinship_fam.R . kinship_last_gen.R . match_fam_founders.R . prune_fam.R . recomb_admix_inds.R . recomb_breaks.R . recomb_chr.R . recomb_fam.R . recomb_geno_inds.R . recomb_hap.R . recomb_haplo_chr.R . recomb_haplo_hap.R . recomb_haplo_ind.R . recomb_haplo_inds.R . recomb_init_founders.R . recomb_last_gen.R . recomb_map_chr.R . recomb_map_fix_ends_chr.R . recomb_map_hap.R . recomb_map_ind.R . recomb_map_inds.R . recomb_map_lengs.R . recomb_map_posg.R . recomb_map_simplify_chr.R . sim_pedigree.R . simfam-package.R . Full simfam package functions and examples
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