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ARTP2

This R package is used for biological pathway analysis and pathway meta-analysis for genome-wide association studies. This is an enhanced version of ARTP on CRAN. An online application of ARTP2 is hosted at https://analysistools.nci.nih.gov/pathway/, where data from the 1000 Genomes Project is provided as genotype reference panel.

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Install

install.packages('ARTP2')

Monthly Downloads

75

Version

0.9.45

License

GPL-2 | GPL-3

Issues

1

Pull Requests

0

Stars

8

Forks

4

Maintainer

Bill Wheeler

Last Published

November 30th, 2018

Functions in ARTP2 (0.9.45)

geno

A vector of file names used in example of rARTP.
subj.id

A vector of subject IDs used in example of sARTP.
warm.start

Performing ARTP2 test with warm start
read.bed

Reading data from binary PLINK files
ref.geno

A dataset used in example of sARTP.
sARTP

ARTP test for summary data
ref.does

Example reference genotype data coded as expected dosages.
meta

Single-marker meta-analysis
exclude.snps

Excluding SNPs from specified regions
pathway

A data frame used in example of rARTP.
data

A dataset used in example of rARTP.
inflation

Computing the genomic control inflation factor from a given numeric vector
rARTP

ARTP test for raw data
ARTP2-package

Pathway and Gene-Level Association Test
options

options
options.default

options.default