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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).

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snpdimensionreductionprincipalcomponentregressionopenblas

7.23 score 16 stars 1 dependents 59 scripts 697 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>.

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6.64 score 21 stars 104 scripts 258 downloads

subSeq - Subsampling of high-throughput sequencing count data

Subsampling of high throughput sequencing count data for use in experiment design and analysis.

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immunooncologysequencingtranscriptionrnaseqgeneexpressiondifferentialexpression

6.56 score 20 stars 30 scripts 406 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>.

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5.52 score 8 stars 41 scripts 310 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.

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snpdimensionreductionprincipalcomponentgenomewideassociation

5.43 score 6 stars 5 scripts 345 downloads