AssocTests: Genetic Association Studies

Some procedures including EIGENSTRAT (a procedure for detecting and correcting for population stratification through searching for the eigenvectors in genetic association studies), PCoC (a procedure for correcting for population stratification through calculating the principal coordinates and the clustering of the subjects), Tracy-Wisdom test (a procedure for detecting the significant eigenvalues of a matrix), distance regression (a procedure for detecting the association between a distance matrix and some independent variants of interest), single-marker test (a procedure for identifying the association between the genotype at a biallelic marker and a trait using the Wald test or the Fisher exact test), MAX3 (a procedure for testing for the association between a single nucleotide polymorphism and a binary phenotype using the maximum value of the three test statistics derived for the recessive, additive, and dominant models), nonparametric trend test (a procedure for testing for the association between a genetic variant and a non-normal distributed quantitative trait based on the nonparametric risk), and nonparametric MAX3 (a procedure for testing for the association between a biallelic single nucleotide polymorphism and a quantitative trait using the maximum value of the three nonparametric trend tests derived for the recessive, additive, and dominant models), which are commonly used in genetic association studies.

Author
Lin Wang [aut], Wei Zhang [aut], Qizhai Li [aut], Weicheng Zhu [ctb]
Date of publication
2015-08-08 15:39:20
Maintainer
Lin Wang <wanglin2009@amss.ac.cn>
License
GPL-2
Version
0.0-3

View on CRAN

Man pages

dr
Distance regression
drS.eg
A toy similarity matrix for dr
eigenstrat
EIGENSTRAT for correcting for population stratification
max3
Maximum Test: maximal value of the three Cochran-Armitage...
nmax3
The NMAX3 based on the nonparametric trend test in a...
npt
The nonparametric trend test based on the nonparametric risk...
pcoc
PCoC for correcting for population stratification
smt
Single-marker test
tw
Tracy-Wisdom test

Files in this package

AssocTests
AssocTests/NAMESPACE
AssocTests/data
AssocTests/data/drS.eg.rda
AssocTests/R
AssocTests/R/SimilarityMatrix.R
AssocTests/R/NMAX3_main.R
AssocTests/R/NPT_main.R
AssocTests/R/MDS.R
AssocTests/R/CorrMatNRTest.R
AssocTests/R/Str2Num.R
AssocTests/R/WaldTest.R
AssocTests/R/FindCNumRandom.R
AssocTests/R/MAX3Sign.R
AssocTests/R/CalculateWAll.R
AssocTests/R/ChangeX.R
AssocTests/R/PCoC_main.R
AssocTests/R/CalculateGapK.R
AssocTests/R/ModifyNormalization.R
AssocTests/R/MAX3_main.R
AssocTests/R/RhombusFormula.R
AssocTests/R/SMT_main.R
AssocTests/R/TrendTest.R
AssocTests/R/TW_main.R
AssocTests/R/ScoreTest.R
AssocTests/R/CalExpect.R
AssocTests/R/EigenStrat_main.R
AssocTests/R/UniformSample.R
AssocTests/R/AssociationTestWithCorrectPS.R
AssocTests/R/UniformTest.R
AssocTests/R/DR_main.R
AssocTests/MD5
AssocTests/DESCRIPTION
AssocTests/man
AssocTests/man/tw.Rd
AssocTests/man/nmax3.Rd
AssocTests/man/smt.Rd
AssocTests/man/max3.Rd
AssocTests/man/dr.Rd
AssocTests/man/eigenstrat.Rd
AssocTests/man/pcoc.Rd
AssocTests/man/drS.eg.Rd
AssocTests/man/npt.Rd