ARTP2: Pathway and Gene-Level Association Test

Pathway and gene level association test using raw data or summary statistics.

Author
Han Zhang, Bill Wheeler, Kai Yu, Yifan Yang, R Core Team
Date of publication
2016-07-11 14:43:11
Maintainer
Han Zhang <han.zhang2@nih.gov>
License
GPL-2 | GPL-3
Version
0.9.30.1
URLs

View on CRAN

Man pages

ARTP2-package
Pathway and Gene-Level Association Test
data
A dataset used in example of 'rARTP'.
exclude.snps
Excluding SNPs from specified regions
geno
A vector of file names used in example of 'rARTP'.
inflation
Computing the genomic control inflation factor from a given...
meta
Single-marker meta-analysis
options
options
options.default
options.default
pathway
A data frame used in example of 'rARTP'.
rARTP
ARTP test for raw data
read.bed
Reading data from binary PLINK files
ref.geno
A dataset used in example of 'sARTP'.
sARTP
ARTP test for summary data
subj.id
A vector of subject IDs used in example of 'sARTP'.
warm.start
Performing ARTP2 test with warm start

Files in this package

ARTP2
ARTP2/inst
ARTP2/inst/extdata
ARTP2/inst/extdata/chr16.fam
ARTP2/inst/extdata/chr17.bed
ARTP2/inst/extdata/FEN1.txt.gz
ARTP2/inst/extdata/chr5.bed
ARTP2/inst/extdata/chr12.bim
ARTP2/inst/extdata/chr22.fam
ARTP2/inst/extdata/chr4.bed
ARTP2/inst/extdata/pathway.txt.gz
ARTP2/inst/extdata/chr4.fam
ARTP2/inst/extdata/chr11.bim
ARTP2/inst/extdata/chr20.bim
ARTP2/inst/extdata/chr1.bed
ARTP2/inst/extdata/chr12.bed
ARTP2/inst/extdata/ref.bed
ARTP2/inst/extdata/chr10.fam
ARTP2/inst/extdata/chr13.bim
ARTP2/inst/extdata/chr14.fam
ARTP2/inst/extdata/chr19.fam
ARTP2/inst/extdata/chr6.bed
ARTP2/inst/extdata/chr20.bed
ARTP2/inst/extdata/chr9.fam
ARTP2/inst/extdata/chr6.bim
ARTP2/inst/extdata/ref.fam
ARTP2/inst/extdata/chr19.bed
ARTP2/inst/extdata/FADS1.txt.gz
ARTP2/inst/extdata/chr12.fam
ARTP2/inst/extdata/CDKN2C.txt.gz
ARTP2/inst/extdata/chr5.bim
ARTP2/inst/extdata/chr8.fam
ARTP2/inst/extdata/chr7.bim
ARTP2/inst/extdata/chr22.bed
ARTP2/inst/extdata/ILF2.txt.gz
ARTP2/inst/extdata/chr8.bim
ARTP2/inst/extdata/chr21.bim
ARTP2/inst/extdata/chr17.fam
ARTP2/inst/extdata/PTK2.txt.gz
ARTP2/inst/extdata/chr2.bed
ARTP2/inst/extdata/chr20.fam
ARTP2/inst/extdata/chr10.bed
ARTP2/inst/extdata/chr21.bed
ARTP2/inst/extdata/CANX.txt.gz
ARTP2/inst/extdata/chr7.fam
ARTP2/inst/extdata/chr3.bim
ARTP2/inst/extdata/chr13.fam
ARTP2/inst/extdata/chr10.bim
ARTP2/inst/extdata/IGF2BP1.txt.gz
ARTP2/inst/extdata/chr9.bim
ARTP2/inst/extdata/SOX12.txt.gz
ARTP2/inst/extdata/GNPAT.txt.gz
ARTP2/inst/extdata/USP30.txt.gz
ARTP2/inst/extdata/chr13.bed
ARTP2/inst/extdata/chr11.fam
ARTP2/inst/extdata/chr7.bed
ARTP2/inst/extdata/chr19.bim
ARTP2/inst/extdata/chr11.bed
ARTP2/inst/extdata/chr1.bim
ARTP2/inst/extdata/chr8.bed
ARTP2/inst/extdata/chr16.bim
ARTP2/inst/extdata/ref.bim
ARTP2/inst/extdata/chr14.bed
ARTP2/inst/extdata/chr1.fam
ARTP2/inst/extdata/chr3.fam
ARTP2/inst/extdata/chr22.bim
ARTP2/inst/extdata/chr9.bed
ARTP2/inst/extdata/chr3.bed
ARTP2/inst/extdata/raw.bed
ARTP2/inst/extdata/NPR1.txt.gz
ARTP2/inst/extdata/chr2.fam
ARTP2/inst/extdata/raw.fam
ARTP2/inst/extdata/chr18.fam
ARTP2/inst/extdata/DCAF7.txt.gz
ARTP2/inst/extdata/chr17.bim
ARTP2/inst/extdata/EIF2C2.txt.gz
ARTP2/inst/extdata/chr15.bim
ARTP2/inst/extdata/chr5.fam
ARTP2/inst/extdata/FADS2.txt.gz
ARTP2/inst/extdata/chr6.fam
ARTP2/inst/extdata/SCYL1.txt.gz
ARTP2/inst/extdata/study2.txt.gz
ARTP2/inst/extdata/raw.bim
ARTP2/inst/extdata/study1.txt.gz
ARTP2/inst/extdata/chr15.fam
ARTP2/inst/extdata/chr16.bed
ARTP2/inst/extdata/chr15.bed
ARTP2/inst/extdata/chr2.bim
ARTP2/inst/extdata/chr18.bed
ARTP2/inst/extdata/chr21.fam
ARTP2/inst/extdata/chr18.bim
ARTP2/inst/extdata/chr14.bim
ARTP2/inst/extdata/chr4.bim
ARTP2/configure.ac
ARTP2/src
ARTP2/src/ReadBED.cpp
ARTP2/src/check_nthread.cpp
ARTP2/src/util.h
ARTP2/src/Makevars.in
ARTP2/src/artp2.cpp
ARTP2/src/Makevars.win
ARTP2/src/check_os.cpp
ARTP2/src/test.cpp
ARTP2/NAMESPACE
ARTP2/NEWS.md
ARTP2/data
ARTP2/data/subj.id.rda
ARTP2/data/pathway.rda
ARTP2/data/ref.geno.rda
ARTP2/data/geno.rda
ARTP2/data/data.rda
ARTP2/R
ARTP2/R/validate.lambda.summaryData.R
ARTP2/R/validate.genofiles.R
ARTP2/R/rawData.dataframe.setup.R
ARTP2/R/create.sub.pathway.R
ARTP2/R/filter.conflictive.snps.R
ARTP2/R/options.validation.R
ARTP2/R/error.try.R
ARTP2/R/load.pathway.definition.R
ARTP2/R/inflation.R
ARTP2/R/cov.svd.R
ARTP2/R/update.pathway.definition.R
ARTP2/R/remove.const.covar.R
ARTP2/R/reformat.reference.path.R
ARTP2/R/reference.type.R
ARTP2/R/trim.deleted.snps.R
ARTP2/R/norm.stat.test.R
ARTP2/R/assign.subject.id.R
ARTP2/R/onAttach.R
ARTP2/R/update.deleted.snps.R
ARTP2/R/create.gene.cutpoint.R
ARTP2/R/options.default.R
ARTP2/R/generate.pathway.pvalue.stat.R
ARTP2/R/validate.family.R
ARTP2/R/update.direction.R
ARTP2/R/create.formula.R
ARTP2/R/convert.method.R
ARTP2/R/update.sf.R
ARTP2/R/artp2.R
ARTP2/R/remove.redendant.covar.R
ARTP2/R/load.summary.files.R
ARTP2/R/check.small.level.R
ARTP2/R/check.misleading.factor.R
ARTP2/R/recover.stat.R
ARTP2/R/map.SNPs.to.genofiles.R
ARTP2/R/meta.R
ARTP2/R/rARTP.R
ARTP2/R/update.setup.R
ARTP2/R/validate.summary.input.R
ARTP2/R/check.os.R
ARTP2/R/validate.pathway.definition.R
ARTP2/R/options.setup.R
ARTP2/R/convert.header.R
ARTP2/R/artp2.chr.R
ARTP2/R/create.super.pathway.R
ARTP2/R/validate.setup.R
ARTP2/R/create.super.pathway.setup.R
ARTP2/R/update.allele.info.R
ARTP2/R/gen.stat.miss.R
ARTP2/R/split.sum.stat.R
ARTP2/R/remove.conflictive.snps.R
ARTP2/R/update.sum.stat.R
ARTP2/R/data.subset.R
ARTP2/R/exclude.snps.R
ARTP2/R/input.type.R
ARTP2/R/sARTP.R
ARTP2/R/update.deleted.genes.R
ARTP2/R/recreate.pathway.R
ARTP2/R/validate.reference.R
ARTP2/R/test.R
ARTP2/R/find.snps.in.regions.R
ARTP2/R/HWE.exact.R
ARTP2/R/summaryData.setup.R
ARTP2/R/validate.outcome.R
ARTP2/R/validate.plinkfiles.R
ARTP2/R/merge.stat.R
ARTP2/R/update.raw.geno.R
ARTP2/R/filter.reference.geno.R
ARTP2/R/update.ref.snps.R
ARTP2/R/data.parse.R
ARTP2/R/create.pathway.cutpoint.R
ARTP2/R/warm.start.R
ARTP2/R/multiple.comparison.summaryData.R
ARTP2/R/rawData.genofiles.setup.R
ARTP2/R/multiple.pathways.setup.R
ARTP2/R/validate.summary.files.R
ARTP2/R/load.pathway.set.R
ARTP2/R/load.reference.allele.R
ARTP2/R/generate.normal.statistics.R
ARTP2/R/validate.sample.size.R
ARTP2/R/map.SNPs.to.plinkfiles.R
ARTP2/R/align.reference.R
ARTP2/R/filter.raw.geno.R
ARTP2/R/validate.lambda.rawData.R
ARTP2/R/extract.conflictive.snps.R
ARTP2/R/complete.sum.stat.R
ARTP2/R/split.pathway.R
ARTP2/R/artp2.select.genes.R
ARTP2/R/turn.off.SNP.filters.R
ARTP2/R/extract.reference.allele.R
ARTP2/R/create.group.R
ARTP2/R/load.summary.statistics.R
ARTP2/R/create.yx.R
ARTP2/R/read.bed.R
ARTP2/R/update.ref.geno.R
ARTP2/R/merge.setups.R
ARTP2/R/load.reference.geno.R
ARTP2/R/validate.covar.R
ARTP2/R/rawData.plinkfiles.setup.R
ARTP2/R/extract.position.information.R
ARTP2/README.md
ARTP2/MD5
ARTP2/DESCRIPTION
ARTP2/configure
ARTP2/man
ARTP2/man/meta.Rd
ARTP2/man/inflation.Rd
ARTP2/man/read.bed.Rd
ARTP2/man/warm.start.Rd
ARTP2/man/options.default.Rd
ARTP2/man/options.Rd
ARTP2/man/ref.geno.Rd
ARTP2/man/sARTP.Rd
ARTP2/man/data.Rd
ARTP2/man/pathway.Rd
ARTP2/man/rARTP.Rd
ARTP2/man/subj.id.Rd
ARTP2/man/exclude.snps.Rd
ARTP2/man/ARTP2-package.Rd
ARTP2/man/geno.Rd