| Title: | EM Bayesian Adaptive LASSO Variational Inference Based GWAS |
| Version: | 0.1.0 |
| 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. |
| Depends: | R (≥ 4.0) |
| Imports: | ggplot2, RColorBrewer |
| Suggests: | rmarkdown, testthat (≥ 3.0.0), roxygen2 |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 7.3.3 |
| NeedsCompilation: | no |
| Packaged: | 2026-04-09 09:49:46 UTC; iasri |
| Author: | 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 <prakash289111@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2026-04-16 08:30:08 UTC |
Build VanRaden Genomic Relationship Matrix
Description
Build VanRaden Genomic Relationship Matrix
Usage
buildGRM(X)
Arguments
X |
Numeric genotype matrix |
Value
GRM matrix
Convert HMP Genotype to Dosage
Description
Convert HMP Genotype to Dosage
Usage
convert_to_dosage(snp_matrix)
Arguments
snp_matrix |
SNP matrix |
Value
Numeric dosage matrix
EM-BALVI GWAS
Description
Performs genome-wide association using expectation-maximization Bayesian adaptive LASSO with variational inference.
Usage
emBALVI(Y, X, B, G, max_iter = 20, tol = 1e-06)
Arguments
Y |
Phenotype vector |
X |
Genotype matrix (numeric dosage) |
B |
Fixed effect design matrix |
G |
Genomic relationship matrix |
max_iter |
Maximum iterations |
tol |
Convergence tolerance |
Value
Data frame of marker effects and p-values
Potato Yield Phenotype Dataset
Description
Phenotypic data used for GWAS analysis in emBALVI.
Usage
phenotypes_potatoyield
Format
A data frame with genotype IDs and yield phenotype.
Source
Real potato yield experiment dataset
Manhattan Plot for emBALVI
Description
Manhattan Plot for emBALVI
Usage
plot_manhattan(results)
Arguments
results |
GWAS result data frame |
Value
A ggplot object
QQ Plot for emBALVI GWAS Results
Description
Generates a Quantile-Quantile (QQ) plot for GWAS p-values.
Usage
plot_qq(results)
Arguments
results |
GWAS result data frame (must contain column 'p') |
Value
A ggplot object
SNP Genotype Dataset (HMP Format)
Description
Raw SNP genotype matrix in HapMap-like format.
Usage
snp_NN_10_hmp
Format
A data frame containing SNP markers and genotype calls.
Source
Real SNP dataset used for EM-BALVI GWAS