tidypopgen

tidypopgen provides a tidy grammar for population genetic analysis of biallelic SNP data in R, enabling genotype data to be read, filtered, and analysed within a single environment.

Key Features:

• Unified workflow: Genotype data can be read, filtered, and analysed within a single R environment without prior data cleaning or setup with other software.
• gen_tibble object structure: A specialised data structure that makes analysis efficient and intuitive.
• Standardised tidy grammar: Clear data manipulation following tidy principles.
• Data management: Supports cleaning and merging datasets.
• Descriptive statistics: Computes basic descriptive statistics for population genetic data.
• Multivariate analysis: Performs multivariate analytical methods.
• Clustering algorithms: Implements clustering algorithms for population structure inference.
• F-statistics: Calculates F-statistics for population genetic analyses.
• Integration with existing R tools: Interfaces with existing tools for population genetic analyses in R.

Scientific Applications:

• Population genetic analysis: Comprehensive analysis of biallelic SNP data for population genetics studies.
• Genome-wide SNP data workflows: Streamlined processing of genome-wide SNP datasets from data assembly through to analysis.
• Population structure inference: Identification of population structure using clustering algorithms and multivariate analysis.
• Human population genetics: Demonstrated using the Human Genome Diversity Project SNP dataset for basic population genetic workflows.

Methodology:

The package implements a tidy grammar approach using a gen_tibble object structure for data representation and manipulation.