Fast Principal Component Analysis for Outlier Detection
Convert a bed to a matrix
pcadapt statistics
Get the principal component the most associated with a genetic marker
Retrieve population names
Population colorization
Neutral Distribution Estimation
Manhattan Plot
Principal Component Analysis for outlier detection
Convert ped files
pcadapt visualization tool
Summary
p-values Q-Q Plot
File Converter
Shiny app
Principal Components Analysis Scores Plot
Principal Components Analysis Scree Plot
Convert vcfR genotype matrices
vcfR-based converter
Write PLINK files
Methods to detect genetic markers involved in biological adaptation. 'pcadapt' provides statistical tools for outlier detection based on Principal Component Analysis. Implements the method described in (Luu, 2016) <DOI:10.1111/1755-0998.12592> and later revised in (Privé, 2020) <DOI:10.1093/molbev/msaa053>.