Overview
SNPutils provides tools for converting numerical genotype data (0, 1, 2) to allele pairs (e.g., “A/G”). The package streamlines genetic data processing workflows by:
- Translating genotype codes into biologically meaningful alleles
- Supporting standard validation rules for SNP data
- Handling both standard SNPs and indels (insertions/deletions)
- Generating TYP format output for downstream analysis
Installation
You can install SNPutils from GitHub:
# Install from GitHub
# install.packages("remotes")
remotes::install_github("LabeoFD/SNPutils")Quick Start
library(SNPutils)
# Load example data
data(example_genotypes)
data(example_annotations)
# Basic workflow
results <- genotype2allele(example_genotypes, example_annotations)
typ_output <- allele2typ(results)
# Check the first few results
head(typ_output)Key Features
- Efficient conversion: Transform numerical codes to nucleotide pairs
- Data validation: Apply standard genetic rules to ensure data quality
- Indel support: Correctly handle insertions and deletions
- Formatted output: Generate standardized TYP format files