PLINK: Whole genome data analysis toolset
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PLINK is a whole genome
association analysis toolset, designed to perform large-scale analyses
in a computationally efficient manner.
PLINK is primarily
developed by Shaun Purcell, although various aspects of the code are
in collaboration with Pak Sham, Ben Neale as well as Mark Daly's group. It
offers the following functions:
Data management
Recode a PED file
Reorder a PED file
Merge two PED files
Extracts subsets (SNPs or individuals)
Flip strand of SNPs
Compress PED data in binary format
Summary statistics for quality control
Allele, genotypes frequencies, HWE tests
Missing genotype rates
Inbreeding, IBS and IBD statistics for individuals and pairs of
individuals
non-Mendelian transmission in family data
Population stratification detection
Complete linkage hierarchical clustering
Handles virtually unlimited numbers of SNPs
Significance test for whether two individuals belong to the same
population
Constrain cluster solution by phenotype and/or specify maximum
cluster size
Perform subsequent association analyses conditional on cluster
solution
Basic association testing
Case/control
Standard allelic test
Cochran-Armitage trend test
Dominant/recessive and general models
Model comparison tests (e.g. general versus multiplicative)
Family-based association (TDT)
Quantitative traits
Asymptotic and empirical p-values
Flexible clustered permutation scheme
Additional tests
Gene-based tests of association
Cumulative rank-order sum statistics
IBS sharing methods
Screen for epistasis (SNP-by-SNP and gene-by-gene)