ARTP2: Pathway and Gene-Level Association Test
Version 0.9.32

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

Browse man pages Browse package API and functions Browse package files

AuthorHan Zhang, Bill Wheeler, Kai Yu, Yifan Yang, R Core Team
Date of publication2017-05-24 07:05:17 UTC
MaintainerHan Zhang <han.zhang2@nih.gov>
LicenseGPL-2 | GPL-3
Version0.9.32
URL https://github.com/zhangh12/ARTP2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ARTP2")

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

Functions

ARTP2 Man page
ARTP2-package Man page
HWE.exact Source code
align.reference Source code
artp2 Source code
artp2.chr Source code
artp2.select.genes Source code
assign.subject.id Source code
check.misleading.factor Source code
check.os Source code
check.small.level Source code
complete.sum.stat Source code
convert.header Source code
convert.method Source code
cov.svd Source code
create.formula Source code
create.gene.cutpoint Source code
create.group Source code
create.pathway.cutpoint Source code
create.sub.pathway Source code
create.super.pathway Source code
create.super.pathway.setup Source code
create.yx Source code
data Man page
data.parse Source code
data.subset Source code
error.try Source code
exclude.snps Man page Source code
extract.conflictive.snps Source code
extract.position.information Source code
extract.reference.allele Source code
filter.conflictive.snps Source code
filter.raw.geno Source code
filter.reference.geno Source code
find.snps.in.regions Source code
gen.stat.miss Source code
generate.normal.statistics Source code
generate.pathway.pvalue.stat Source code
geno Man page
inflation Man page Source code
input.type Source code
load.pathway.definition Source code
load.pathway.set Source code
load.reference.allele Source code
load.reference.geno Source code
load.summary.files Source code
load.summary.statistics Source code
map.SNPs.to.genofiles Source code
map.SNPs.to.plinkfiles Source code
merge.setups Source code
merge.stat Source code
meta Man page Source code
multiple.comparison.summaryData Source code
multiple.pathways.setup Source code
norm.stat.test Source code
onAttach Source code
options Man page
options.default Man page Source code
options.setup Source code
options.validation Source code
pathway Man page
rARTP Man page Source code
rawData.dataframe.setup Source code
rawData.genofiles.setup Source code
rawData.plinkfiles.setup Source code
read.bed Man page Source code
recover.stat Source code
recreate.pathway Source code
ref.geno Man page
reference.type Source code
reformat.reference.path Source code
remove.conflictive.snps Source code
remove.const.covar Source code
remove.redendant.covar Source code
sARTP Man page Source code
split.pathway Source code
split.sum.stat Source code
subj.id Man page
summaryData.setup Source code
test Source code
trim.deleted.snps Source code
turn.off.SNP.filters Source code
update.allele.info Source code
update.deleted.genes Source code
update.deleted.snps Source code
update.direction Source code
update.pathway.definition Source code
update.raw.geno Source code
update.ref.geno Source code
update.ref.snps Source code
update.setup Source code
update.sf Source code
update.sum.stat Source code
validate.covar Source code
validate.family Source code
validate.genofiles Source code
validate.lambda.rawData Source code
validate.lambda.summaryData Source code
validate.outcome Source code
validate.pathway.definition Source code
validate.plinkfiles Source code
validate.reference Source code
validate.sample.size Source code
validate.setup Source code
validate.summary.files Source code
validate.summary.input Source code
warm.start Man page Source code

Files

inst
inst/extdata
inst/extdata/chr16.fam
inst/extdata/chr17.bed
inst/extdata/FEN1.txt.gz
inst/extdata/chr5.bed
inst/extdata/chr12.bim
inst/extdata/chr22.fam
inst/extdata/chr4.bed
inst/extdata/pathway.txt.gz
inst/extdata/chr4.fam
inst/extdata/chr11.bim
inst/extdata/chr20.bim
inst/extdata/chr1.bed
inst/extdata/chr12.bed
inst/extdata/ref.bed
inst/extdata/chr10.fam
inst/extdata/chr13.bim
inst/extdata/chr14.fam
inst/extdata/chr19.fam
inst/extdata/chr6.bed
inst/extdata/chr20.bed
inst/extdata/chr9.fam
inst/extdata/chr6.bim
inst/extdata/ref.fam
inst/extdata/chr19.bed
inst/extdata/FADS1.txt.gz
inst/extdata/chr12.fam
inst/extdata/CDKN2C.txt.gz
inst/extdata/chr5.bim
inst/extdata/chr8.fam
inst/extdata/chr7.bim
inst/extdata/chr22.bed
inst/extdata/ILF2.txt.gz
inst/extdata/chr8.bim
inst/extdata/chr21.bim
inst/extdata/chr17.fam
inst/extdata/PTK2.txt.gz
inst/extdata/chr2.bed
inst/extdata/chr20.fam
inst/extdata/chr10.bed
inst/extdata/chr21.bed
inst/extdata/CANX.txt.gz
inst/extdata/chr7.fam
inst/extdata/chr3.bim
inst/extdata/chr13.fam
inst/extdata/chr10.bim
inst/extdata/IGF2BP1.txt.gz
inst/extdata/chr9.bim
inst/extdata/SOX12.txt.gz
inst/extdata/GNPAT.txt.gz
inst/extdata/USP30.txt.gz
inst/extdata/chr13.bed
inst/extdata/chr11.fam
inst/extdata/chr7.bed
inst/extdata/chr19.bim
inst/extdata/chr11.bed
inst/extdata/chr1.bim
inst/extdata/chr8.bed
inst/extdata/chr16.bim
inst/extdata/ref.bim
inst/extdata/chr14.bed
inst/extdata/chr1.fam
inst/extdata/chr3.fam
inst/extdata/chr22.bim
inst/extdata/chr9.bed
inst/extdata/chr3.bed
inst/extdata/raw.bed
inst/extdata/NPR1.txt.gz
inst/extdata/chr2.fam
inst/extdata/raw.fam
inst/extdata/chr18.fam
inst/extdata/DCAF7.txt.gz
inst/extdata/chr17.bim
inst/extdata/EIF2C2.txt.gz
inst/extdata/chr15.bim
inst/extdata/chr5.fam
inst/extdata/FADS2.txt.gz
inst/extdata/chr6.fam
inst/extdata/SCYL1.txt.gz
inst/extdata/study2.txt.gz
inst/extdata/raw.bim
inst/extdata/study1.txt.gz
inst/extdata/chr15.fam
inst/extdata/chr16.bed
inst/extdata/chr15.bed
inst/extdata/chr2.bim
inst/extdata/chr18.bed
inst/extdata/chr21.fam
inst/extdata/chr18.bim
inst/extdata/chr14.bim
inst/extdata/chr4.bim
configure.ac
src
src/artp2_main.cpp
src/ReadBED.cpp
src/check_nthread.cpp
src/util.h
src/Makevars.in
src/ARTP2_init.c
src/test_c.cpp
src/Makevars.win
src/check_os.cpp
NAMESPACE
NEWS.md
data
data/subj.id.rda
data/pathway.rda
data/ref.geno.rda
data/geno.rda
data/data.rda
R
R/validate.lambda.summaryData.R
R/validate.genofiles.R
R/rawData.dataframe.setup.R
R/create.sub.pathway.R
R/filter.conflictive.snps.R
R/options.validation.R
R/error.try.R
R/load.pathway.definition.R
R/inflation.R
R/cov.svd.R
R/update.pathway.definition.R
R/remove.const.covar.R
R/reformat.reference.path.R
R/reference.type.R
R/trim.deleted.snps.R
R/norm.stat.test.R
R/assign.subject.id.R
R/onAttach.R
R/update.deleted.snps.R
R/create.gene.cutpoint.R
R/options.default.R
R/generate.pathway.pvalue.stat.R
R/validate.family.R
R/update.direction.R
R/create.formula.R
R/convert.method.R
R/update.sf.R
R/artp2.R
R/remove.redendant.covar.R
R/load.summary.files.R
R/check.small.level.R
R/check.misleading.factor.R
R/recover.stat.R
R/map.SNPs.to.genofiles.R
R/meta.R
R/rARTP.R
R/update.setup.R
R/validate.summary.input.R
R/check.os.R
R/validate.pathway.definition.R
R/options.setup.R
R/convert.header.R
R/artp2.chr.R
R/create.super.pathway.R
R/validate.setup.R
R/create.super.pathway.setup.R
R/update.allele.info.R
R/gen.stat.miss.R
R/split.sum.stat.R
R/remove.conflictive.snps.R
R/update.sum.stat.R
R/data.subset.R
R/exclude.snps.R
R/input.type.R
R/sARTP.R
R/update.deleted.genes.R
R/recreate.pathway.R
R/validate.reference.R
R/test.R
R/find.snps.in.regions.R
R/HWE.exact.R
R/summaryData.setup.R
R/validate.outcome.R
R/validate.plinkfiles.R
R/merge.stat.R
R/update.raw.geno.R
R/filter.reference.geno.R
R/update.ref.snps.R
R/data.parse.R
R/create.pathway.cutpoint.R
R/warm.start.R
R/multiple.comparison.summaryData.R
R/rawData.genofiles.setup.R
R/multiple.pathways.setup.R
R/validate.summary.files.R
R/load.pathway.set.R
R/load.reference.allele.R
R/generate.normal.statistics.R
R/validate.sample.size.R
R/map.SNPs.to.plinkfiles.R
R/align.reference.R
R/filter.raw.geno.R
R/validate.lambda.rawData.R
R/extract.conflictive.snps.R
R/complete.sum.stat.R
R/split.pathway.R
R/artp2.select.genes.R
R/turn.off.SNP.filters.R
R/extract.reference.allele.R
R/create.group.R
R/load.summary.statistics.R
R/create.yx.R
R/read.bed.R
R/update.ref.geno.R
R/merge.setups.R
R/load.reference.geno.R
R/validate.covar.R
R/rawData.plinkfiles.setup.R
R/extract.position.information.R
README.md
MD5
DESCRIPTION
configure
man
man/meta.Rd
man/inflation.Rd
man/read.bed.Rd
man/warm.start.Rd
man/options.default.Rd
man/options.Rd
man/ref.geno.Rd
man/sARTP.Rd
man/data.Rd
man/pathway.Rd
man/rARTP.Rd
man/subj.id.Rd
man/exclude.snps.Rd
man/ARTP2-package.Rd
man/geno.Rd
cleanup
ARTP2 documentation built on May 24, 2017, 9:02 a.m.