Files in zhangh12/ARTP3
Pathway and Gene-Level Association Test
.Rbuildignore
.gitignore
ARTP2.Rproj
DESCRIPTION
NAMESPACE
NEWS.md
R/HWE.exact.R
R/align.ambig.meta.R
R/align.ambig.snps.R
R/align.ambig.study.R
R/align.reference.R
R/ambig.check.data.R
R/ambig.snps.R
R/artp2.R
R/artp2.chr.R
R/artp2.select.genes.R
R/assign.subject.id.R
R/check.misleading.factor.R
R/check.os.R
R/check.small.level.R
R/complete.sum.stat.R
R/convert.header.R
R/convert.method.R
R/cov.svd.R
R/create.formula.R
R/create.gene.cutpoint.R
R/create.group.R
R/create.pathway.cutpoint.R
R/create.sub.pathway.R
R/create.super.pathway.R
R/create.super.pathway.setup.R
R/create.yx.R
R/data.parse.R
R/data.subset.R
R/error.try.R
R/exclude.snps.R
R/expand_pathway.R
R/extract.conflictive.snps.R
R/extract.position.information.R
R/extract.reference.allele.R
R/filter.ambig.snps.R
R/filter.conflictive.snps.R
R/filter.raw.geno.R
R/filter.reference.geno.R
R/find.marg.signal.R
R/find.snps.in.regions.R
R/gen.stat.miss.R
R/generate.normal.statistics.R
R/generate.pathway.pvalue.stat.R
R/inflation.R
R/input.type.R
R/load.file.R
R/load.pathway.definition.R
R/load.pathway.set.R
R/load.reference.allele.R
R/load.reference.geno.R
R/load.summary.files.R
R/load.summary.statistics.R
R/makeVector.R
R/map.SNPs.to.genofiles.R
R/map.SNPs.to.plinkfiles.R
R/merge.setups.R
R/merge.stat.R
R/meta.R
R/multiple.comparison.summaryData.R
R/multiple.pathways.setup.R
R/norm.stat.test.R
R/onAttach.R
R/options.default.R
R/options.setup.R
R/options.validation.R
R/parseDelimVec.R
R/rARTP.R
R/rawData.dataframe.setup.R
R/rawData.genofiles.setup.R
R/rawData.plinkfiles.setup.R
R/read.bed.R
R/recover.stat.R
R/recreate.pathway.R
R/reference.type.R
R/reformat.reference.path.R
R/reformat.snps.R
R/remove.conflictive.snps.R
R/remove.const.covar.R
R/remove.redendant.covar.R
R/removeWhiteSpace.R
R/sARTP.R
R/split.pathway.R
R/split.sum.stat.R
R/summaryData.setup.R
R/test.R
R/tester.R
R/trim.deleted.snps.R
R/turn.off.SNP.filters.R
R/update.allele.info.R
R/update.deleted.genes.R
R/update.deleted.snps.R
R/update.direction.R
R/update.pathway.definition.R
R/update.raw.geno.R
R/update.ref.geno.R
R/update.ref.snps.R
R/update.setup.R
R/update.sf.R
R/update.sum.stat.R
R/validate.covar.R
R/validate.family.R
R/validate.genofiles.R
R/validate.lambda.rawData.R
R/validate.lambda.summaryData.R
R/validate.outcome.R
R/validate.pathway.definition.R
R/validate.plinkfiles.R
R/validate.reference.R
R/validate.sample.size.R
R/validate.setup.R
R/validate.summary.files.R
R/validate.summary.input.R
R/warm.start.R
README.md
cleanup
configure
configure.ac
data/data.rda
data/geno.rda
data/pathway.rda
data/ref.does.rda
data/ref.geno.rda
data/subj.id.rda
inst/extdata/CANX.txt.gz
inst/extdata/CDKN2C.txt.gz
inst/extdata/DCAF7.txt.gz
inst/extdata/EIF2C2.txt.gz
inst/extdata/FADS1.txt.gz
inst/extdata/FADS2.txt.gz
inst/extdata/FEN1.txt.gz
inst/extdata/GNPAT.txt.gz
inst/extdata/IGF2BP1.txt.gz
inst/extdata/ILF2.txt.gz
inst/extdata/NPR1.txt.gz
inst/extdata/PTK2.txt.gz
inst/extdata/SCYL1.txt.gz
inst/extdata/SOX12.txt.gz
inst/extdata/USP30.txt.gz
inst/extdata/chr1.bed
inst/extdata/chr1.bim
inst/extdata/chr1.fam
inst/extdata/chr10.bed
inst/extdata/chr10.bim
inst/extdata/chr10.fam
inst/extdata/chr11.bed
inst/extdata/chr11.bim
inst/extdata/chr11.fam
inst/extdata/chr12.bed
inst/extdata/chr12.bim
inst/extdata/chr12.fam
inst/extdata/chr13.bed
inst/extdata/chr13.bim
inst/extdata/chr13.fam
inst/extdata/chr14.bed
inst/extdata/chr14.bim
inst/extdata/chr14.fam
inst/extdata/chr15.bed
inst/extdata/chr15.bim
inst/extdata/chr15.fam
inst/extdata/chr16.bed
inst/extdata/chr16.bim
inst/extdata/chr16.fam
inst/extdata/chr17.bed
inst/extdata/chr17.bim
inst/extdata/chr17.fam
inst/extdata/chr18.bed
inst/extdata/chr18.bim
inst/extdata/chr18.fam
inst/extdata/chr19.bed
inst/extdata/chr19.bim
inst/extdata/chr19.fam
inst/extdata/chr2.bed
inst/extdata/chr2.bim
inst/extdata/chr2.fam
inst/extdata/chr20.bed
inst/extdata/chr20.bim
inst/extdata/chr20.fam
inst/extdata/chr21.bed
inst/extdata/chr21.bim
inst/extdata/chr21.fam
inst/extdata/chr22.bed
inst/extdata/chr22.bim
inst/extdata/chr22.fam
inst/extdata/chr3.bed
inst/extdata/chr3.bim
inst/extdata/chr3.fam
inst/extdata/chr4.bed
inst/extdata/chr4.bim
inst/extdata/chr4.fam
inst/extdata/chr5.bed
inst/extdata/chr5.bim
inst/extdata/chr5.fam
inst/extdata/chr6.bed
inst/extdata/chr6.bim
inst/extdata/chr6.fam
inst/extdata/chr7.bed
inst/extdata/chr7.bim
inst/extdata/chr7.fam
inst/extdata/chr8.bed
inst/extdata/chr8.bim
inst/extdata/chr8.fam
inst/extdata/chr9.bed
inst/extdata/chr9.bim
inst/extdata/chr9.fam
inst/extdata/pathway.txt.gz
inst/extdata/raw.bed
inst/extdata/raw.bim
inst/extdata/raw.fam
inst/extdata/ref.bed
inst/extdata/ref.bim
inst/extdata/ref.fam
inst/extdata/study1.txt.gz
inst/extdata/study2.txt.gz
man/ARTP2-package.Rd
man/data.Rd
man/exclude.snps.Rd
man/geno.Rd
man/inflation.Rd
man/meta.Rd
man/options.Rd
man/options.default.Rd
man/pathway.Rd
man/rARTP.Rd
man/read.bed.Rd
man/ref.does.Rd
man/ref.geno.Rd
man/sARTP.Rd
man/subj.id.Rd
man/warm.start.Rd
src/ARTP2_init.c
src/Makevars
src/Makevars.in
src/Makevars.win
src/ReadBED.cpp
src/artp2_main.cpp
src/check_nthread.cpp
src/check_os.cpp
src/test_c.cpp
src/util.h
