歡迎關(guān)注公眾號(hào)：oddxix
背景
Plink是一個(gè)免費(fèi)稚虎、開(kāi)源的全基因組關(guān)聯(lián)分析工具集，用于執(zhí)行基本范圍的、大規(guī)模分析計(jì)算的有效方式枕屉。PLINK的重點(diǎn)是對(duì)基因型/表型數(shù)據(jù)的分析，因此不支持此前的步驟（例如鲤氢，研究設(shè)計(jì)和計(jì)劃搀擂，從原始數(shù)據(jù)生成基因型或CNV調(diào)用）。通過(guò)與gPLINK和Haploview集成卷玉，可以為后續(xù)的可視化哨颂，注釋和結(jié)果存儲(chǔ)提供支持。
plink的主要功能：數(shù)據(jù)處理揍庄，質(zhì)量控制的基本統(tǒng)計(jì)咆蒿，群體分層分析，單位點(diǎn)的基本關(guān)聯(lián)分析，家系數(shù)據(jù)的傳遞不平衡檢驗(yàn)沃测，多點(diǎn)連鎖分析缭黔，單倍體關(guān)聯(lián)分析，拷貝數(shù)變異分析蒂破，Meta分析等等馏谨。
Data management數(shù)據(jù)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質(zhì)量控制的摘要統(tǒng)計(jì)
- 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人口分層檢測(cè)
- 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基本關(guān)聯(lián)測(cè)試
- 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多標(biāo)記預(yù)測(cè)因子，單倍型測(cè)試
- 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拷貝數(shù)變異分析
- 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其他測(cè)試
- 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結(jié)果注釋和報(bào)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
參考：http://zzz.bwh.harvard.edu/plink/index.shtml
轉(zhuǎn)載請(qǐng)注明出處：
簡(jiǎn)書(shū)作者：oddxix
歡迎關(guān)注公眾號(hào)：oddxix
