FREGAT: Family REGional Association Tests
Version 1.0.3

Fast regional association analysis of quantitative traits for family-based and population studies.

Browse man pages Browse package API and functions Browse package files

AuthorNadezhda M. Belonogova <belon@bionet.nsc.ru> and Gulnara R. Svishcheva <gulsvi@mail.ru>, with contributions from: Seunggeun Lee (kernel functions), Pierre Lafaye de Micheaux ('davies' method), Thomas Lumley ('kuonen' method), James O. Ramsay (functional data analysis functions), David Clayton ('read.plink' function) and Brian Ripley ('ginv' function)
Date of publication2017-04-21 05:57:18 UTC
MaintainerNadezhda M. Belonogova <belon@bionet.nsc.ru>
LicenseGPL-3
Version1.0.3
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("FREGAT")

Man pages

example.data: A small example data set
famBT: Family Burden Test
famFLM: family Functional Linear Model
FFBSKAT: Fast Family-Based SKAT
FREGAT-package: FREGAT: Family REGional Association Tests
MLR: multiple linear regression
null: Fitting the null model
read.plink: Read a PLINK binary data file
single.point: A single-point association test

Functions

FFBSKAT Man page
FREGAT-package Man page
Get_Lambda Source code
Get_Liu_PVal.MOD Source code
Get_Liu_PVal.MOD.Lambda Source code
Get_Liu_PVal.MOD.Lambda.Zero Source code
Get_Liu_Params Source code
Get_Liu_Params_Mod Source code
Get_Liu_Params_Mod_Lambda Source code
Get_PValue.Lambda Source code
Lfd Source code
MLR Man page
NullMixedModel Source code
SKAT_Optiaml_Each_Q Source code
SKAT_Optimal_Get_Pvalue Source code
SKAT_Optimal_Integrate_Func_Davies Source code
SKAT_Optimal_Integrate_Func_Kuonen Source code
SKAT_Optimal_Integrate_Func_Liu Source code
SKAT_Optimal_PValue_Davies_Kuonen Source code
SKAT_Optimal_PValue_Liu Source code
SKAT_Optimal_Param Source code
SnpMatrix2numeric Source code
analyze.region Source code
analyze.single Source code
basisfd Source code
bsplineS Source code
call_Kernel_2wayIX Source code
call_Kernel_IBS Source code
call_Kernel_IBS_Weight Source code
check.basis Source code
check.cores Source code
check.covariates Source code
check.geno Source code
check.ini Source code
check.method Source code
check.nullmod Source code
check.regions Source code
check.rho Source code
check.spec.famFLM Source code
check.spec.famSKAT Source code
check.weights Source code
create.bspline.basis Source code
create.constant.basis Source code
create.fourier.basis Source code
davies Source code
eval.basis Source code
eval.fd Source code
example.data Man page
famBT Man page
famFLM Man page
fd Source code
fd2list Source code
fdchk Source code
fitted.fdSmooth Source code
flipper Source code
fourier Source code
genodata Man page
genotypes Source code
getbasismatrix Source code
ginv Source code
hasIndex Source code
inprod Source code
inprod.bspline Source code
int2Lfd Source code
is.eqbasis Source code
isURL Source code
kin Man page
knotmultchk Source code
local.file.exists Source code
lskmTest.GetKernel Source code
make.call Source code
null Man page
pchisqsum Source code
phenodata Man page
polyprod Source code
ppBspline Source code
ppderiv Source code
predict.fd Source code
predict.fdPar Source code
predict.fdSmooth Source code
pval.MLR Source code
pval.famBT Source code
pval.famFLM Source code
pval.famSKAT Source code
pval.famSKATO Source code
rangechk Source code
read.plink Man page Source code
read.plink.names Source code
read.plink.region Source code
read.vcf Source code
read.vcf.pos Source code
residuals.fdSmooth Source code
saddle Source code
single.point Man page
snpdata Man page
subset.SnpMatrix Source code
tau.fun Source code
tau3 Source code
tau3.old Source code

Files

inst
inst/testfiles
inst/testfiles/sample.bed
inst/testfiles/sample.fam
inst/testfiles/sample.bim
inst/testfiles/1000g.phase1.20110521.CFH.var.anno.vcf.gz
inst/testfiles/refFlat_hg19_6col.txt.gz
inst/testfiles/sample.info
inst/testfiles/1000g.phase1.20110521.CFH.var.anno.vcf.gz.tbi
inst/doc
inst/doc/FREGAT-manual.pdf
src
src/asnum.c
src/uncertain.c
src/ruben.cpp
src/uncertain.h
src/subset.c
src/FREGAT_init.c
src/Rmissing.h
src/kernel_func.c
src/qfc.cpp
src/plink.c
NAMESPACE
data
data/example.data.RData
R
R/PVE.R
R/create.constant.basis.R
R/polylik.R
R/create.bspline.basis.R
R/int2Lfd.R
R/SnpMatrix.R
R/eval.fd.R
R/eval.basis.R
R/fourier.R
R/read.plink.R
R/fd2list.R
R/chisqsum.R
R/genotypes.R
R/function.R
R/seqminer.R
R/create.fourier.basis.R
R/analyze.R
R/is.eqbasis.R
R/check.input.R
R/rangechk.R
R/ppBspline.R
R/bsplineS.R
R/ppderiv.R
R/fd.R
R/inprod.R
R/inprod.bspline.R
R/kernels.R
R/KMTest_Optimal.R
R/Lfd.R
R/fixed.effects.R
R/polyprod.R
R/random.effects.R
R/single.point.R
R/basisfd.R
R/davies.R
R/check.spec.R
R/getbasismatrix.R
R/null.R
R/do.regional.R
R/main.R
MD5
DESCRIPTION
man
man/single.point.rd
man/example.data.rd
man/famBT.rd
man/read.plink.rd
man/null.rd
man/MLR.rd
man/famFLM.rd
man/FFBSKAT.rd
man/FREGAT-package.rd
CHANGES
FREGAT documentation built on May 19, 2017, 3:59 p.m.