genio - Genetics Input/Output Functions

Implements readers and writers for file formats associated with genetics data. Reading and writing Plink BED/BIM/FAM and GCTA binary GRM formats is fully supported, including a lightning-fast BED reader and writer implementations. Other functions are 'readr' wrappers that are more constrained, user-friendly, and efficient for these particular applications; handles Plink and Eigenstrat tables (FAM, BIM, IND, and SNP files). There are also make functions for FAM and BIM tables with default values to go with simulated genotype data.

Last updated 3 months ago

7.42 score 17 stars 3 packages 173 scripts 736 downloads

lfa - Logistic Factor Analysis for Categorical Data

Logistic Factor Analysis is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter. The main method estimates genetic population structure from genotype data. There are also methods for estimating individual-specific allele frequencies using the population structure. Lastly, a structured Hardy-Weinberg equilibrium (HWE) test is developed, which quantifies the goodness of fit of the genotype data to the estimated population structure, via the estimated individual-specific allele frequencies (all of which generalizes traditional HWE tests).

Last updated 24 days ago

snpdimensionreductionprincipalcomponentregression

7.02 score 16 stars 1 packages 54 scripts 605 downloads

popkin - Estimate Kinship and FST under Arbitrary Population Structure

Provides functions to estimate the kinship matrix of individuals from a large set of biallelic SNPs, and extract inbreeding coefficients and the generalized FST (Wright's fixation index). Method described in Ochoa and Storey (2021) <doi:10.1371/journal.pgen.1009241>.

Last updated 2 months ago

6.08 score 19 stars 64 scripts 312 downloads

bnpsd - Simulate Genotypes from the BN-PSD Admixture Model

The Pritchard-Stephens-Donnelly (PSD) admixture model has k intermediate subpopulations from which n individuals draw their alleles dictated by their individual-specific admixture proportions. The BN-PSD model additionally imposes the Balding-Nichols (BN) allele frequency model to the intermediate populations, which therefore evolved independently from a common ancestral population T with subpopulation-specific FST (Wright's fixation index) parameters. The BN-PSD model can be used to yield complex population structures. This simulation approach is now extended to subpopulations related by a tree. Method described in Ochoa and Storey (2021) <doi:10.1371/journal.pgen.1009241>.

Last updated 1 years ago

5.42 score 8 stars 33 scripts 340 downloads

gcatest - Genotype Conditional Association TEST

GCAT is an association test for genome wide association studies that controls for population structure under a general class of trait models. This test conditions on the trait, which makes it immune to confounding by unmodeled environmental factors. Population structure is modeled via logistic factors, which are estimated using the `lfa` package.

Last updated 24 days ago

snpdimensionreductionprincipalcomponentgenomewideassociation

5.18 score 5 stars 4 scripts 240 downloads

simtrait - Simulate Complex Traits from Genotypes

Simulate complex traits given a SNP genotype matrix and model parameters (the desired heritability, optional environment group effects, number of causal loci, and either the true ancestral allele frequencies used to generate the genotypes or the mean kinship for a real dataset). Emphasis is on avoiding common biases due to the use of estimated allele frequencies. The code selects random loci to be causal, constructs coefficients for these loci and random independent non-genetic effects, and can optionally generate random group effects. Traits can follow three models: random coefficients, fixed effect sizes, and infinitesimal (multivariate normal). GWAS method benchmarking functions are also provided. Described in Yao and Ochoa (2023) <doi:10.7554/eLife.79238>.

Last updated 2 days ago

5.10 score 4 stars 21 scripts 141 downloads

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>.

Last updated 3 days ago

4.89 score 2 stars 11 scripts 148 downloads