Plink_1.介绍

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背景

Plink是一个免费、开源的全基因组关联分析工具集，用于执行基本范围的、大规模分析计算的有效方式。PLINK的重点是对基因型/表型数据的分析，因此不支持此前的步骤（例如，研究设计和计划，从原始数据生成基因型或CNV调用）。通过与gPLINK和Haploview集成，可以为后续的可视化，注释和结果存储提供支持。
plink的主要功能：数据处理，质量控制的基本统计，群体分层分析，单位点的基本关联分析，家系数据的传递不平衡检验，多点连锁分析，单倍体关联分析，拷贝数变异分析，Meta分析等等。

Data management数据管理

• Read data in a variety of formats
• Recode and reorder files
• Merge two or more files
• Extracts subsets (SNPs or individuals)
• Flip strand of SNPs
• Compress data in a binary file format

Summary statistics for quality control质量控制的摘要统计

• 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
• Sex checks based on X chromosome SNPs
• Tests of non-random genotyping failure

Population stratification detection人口分层检测

• Complete linkage hierarchical clustering
• Handles virtually unlimited numbers of SNPs
• Multidimensional scaling analysis to visualise substructure
• Significance test for whether two individuals belong to the same population
• Constrain cluster solution by phenotype, cluster size and/or external matching criteria
• Perform subsequent association analyses conditional on cluster solution

Basic association testing基本关联测试

• Case/control

  Standard allelic test
  Fisher's exact test
  Cochran-Armitage trend test
  Mantel-Haenszel and Breslow-Day tests for stratified samples
  Dominant/recessive and general models
  Model comparison tests (e.g. general versus multiplicative)

• Family-based association (TDT, sibship tests)
• Quantitative traits, association and interaction
• Association conditional on one or more SNPs
• Asymptotic and empirical p-values
• Flexible clustered permutation scheme
• Analysis of genotype probability data and fractional allele coounts (post-imputation)

Multimarker predictors, haplotypic tests多标记预测因子，单倍型测试

• Suite of flexible, conditional haplotype tests
• Case/control and TDT association on the probabilistic haplotype phase
• A set of proxy associaiton" methods to study single SNP associations in their local haplotypic context
• Imputation heuristic, to test untyped SNPs given a reference panel

Copy number variant analysis拷贝数变异分析

• Joint SNP and CNV tests for common copy number variants
• Filtering and summary procedures for segmental (rare) CNV data
• Case/control comparison tests for global CNV properties
• Permutation-based association procedure for identifying specific loci

Additional tests其他测试

• Gene-based tests of association
• Screen for epistasis
• Gene-environment interaction with continuous and dichotomous environments

Meta-analysisMeta分析

• Automatically combine several generically-formatted summary files, for millions of SNPs
• Fixed and random effects models

Result annotation and reporting结果注释和报告

• Post-analysis annotation of result files
• LD-based and region-based grouping of results across multiple studies

Additional features附加功能

• Extensible with via R function plug-ins
• Web-based SNP and gene annotation lookup feature
• Simple SNP simulation feature
• ID helper tools, for tracking and working with project data
• See the main documentation for full list of features

参考：http://zzz.bwh.harvard.edu/plink/index.shtml

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