| Title: | EM Bayesian Adaptive LASSO Variational Inference Based GWAS |
|---|---|
| Description: | Performs Genome-Wide Association Study (GWAS) analysis using Expectation-Maximization Bayesian Adaptive LASSO with Variational Inference (emBALVI). Includes genotype preprocessing, genomic relationship matrix construction, GWAS analysis, Manhattan and QQ plotting.s. |
| Authors: | Prakash Kumar [aut, cre], Himadri Sekhar Roy [aut], Ranjit Kumar Paul [aut], Md. Yeasin [aut], Neeraj Budhlakoti [aut], Sunil Kumar Yadav [aut], Amrit Kumar Paul [aut] |
| Maintainer: | Prakash Kumar <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.1.0 |
| Built: | 2026-05-16 08:52:29 UTC |
| Source: | https://github.com/cran/emBALVI |
Build VanRaden Genomic Relationship Matrix
buildGRM(X)buildGRM(X)
X |
Numeric genotype matrix |
GRM matrix
Convert HMP Genotype to Dosage
convert_to_dosage(snp_matrix)convert_to_dosage(snp_matrix)
snp_matrix |
SNP matrix |
Numeric dosage matrix
Performs genome-wide association using expectation-maximization Bayesian adaptive LASSO with variational inference.
emBALVI(Y, X, B, G, max_iter = 20, tol = 1e-06)emBALVI(Y, X, B, G, max_iter = 20, tol = 1e-06)
Y |
Phenotype vector |
X |
Genotype matrix (numeric dosage) |
B |
Fixed effect design matrix |
G |
Genomic relationship matrix |
max_iter |
Maximum iterations |
tol |
Convergence tolerance |
Data frame of marker effects and p-values
Phenotypic data used for GWAS analysis in emBALVI.
phenotypes_potatoyieldphenotypes_potatoyield
A data frame with genotype IDs and yield phenotype.
Real potato yield experiment dataset
Manhattan Plot for emBALVI
plot_manhattan(results)plot_manhattan(results)
results |
GWAS result data frame |
A ggplot object
Generates a Quantile-Quantile (QQ) plot for GWAS p-values.
plot_qq(results)plot_qq(results)
results |
GWAS result data frame (must contain column 'p') |
A ggplot object
Raw SNP genotype matrix in HapMap-like format.
snp_NN_10_hmpsnp_NN_10_hmp
A data frame containing SNP markers and genotype calls.
Real SNP dataset used for EM-BALVI GWAS