李启寨
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Software

R codes

 

1) Association Tests in Genetic Association Studies:

                  R packages AssTest

The function index of the package AssocTest is listed as follows:

• eigenstrat(): EIGENSTRAT for correcting for population stratification

• mds(): Multi-dimension scaling for correcting for population stratification

• tw(): Tracy-Wisdom test, the significance of the eigenvalues

• dr(): Distance regression

• smt(): Single-marker test 

• max3(): Maximum Test: maximal values of the three Cochran-Armitage trend tests under the recessive,additive, and dominant models with or without considering covariates such as population stratification

• npt(): The nonparametric trend test based on the nonparametric risk under a given genetic model

• nmax3(): The NMAX3 test which is the maximum of the three nonparametric trend tests under the recessive, additive, and dominant models, respectively, in a quantitative trait association study

 

2) Adaptively Combined P-Value in Pathway Analysis: 

                 R codes: ARTP

Yu K, Li Q, Bergen AW, Pfeiffer RM, Rosenberg PS, Caporaso N, Kraft P, Chatterjee N 2009) Pathway analysis by adaptive combination of P-values. Genet Epidemiol 8,700-709.   

3) Group combined p-values method to do multipe-SNP assocation studies:

                 R codes: GCP 

    Hu X, Zhang W, Zhang S, Ma S, Li Q. (2016). Group-combined P-values with applications to genetic association studies.Bioinformatics.32(18):2737-43.

 

4) A model-embedded trend test in genetic association studies: 

                 Rcodes: MET 

 

5) An efficient procedure in study of pleiotropic genetic associations:

                 R codes: GATE 

 

时间:2015-10-27  来源: 文本大小:【 |  | 】  【打印
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