ARTP: Gene and Pathway p-values computed using the Adaptive Rank Truncated Product

A package for calculating gene and pathway p-values using the Adaptive Rank Truncated Product test

Author
Kai Yu, Qizhai Li and William Wheeler
Date of publication
2014-02-20 18:51:03
Maintainer
Bill Wheeler <wheelerb@imsweb.com>
License
GPL-2
Version
2.0.4

View on CRAN

Man pages

ARTP
Gene and pathway p-values using the Adaptive Rank Truncated...
ARTP_pathway
Gene and pathway p-values using ARTP
gene.list
List to describe the gene-SNP file
gene_SNP_data
Gene-SNP data
geno_data
Sample genotype data
obs_pvalues
Observed p-values
perm_pvalues
Permutation p-values
pheno_data
Sample covariate and response data
pheno.list
List to describe the covariate and outcome data
plot_genes
Gene Plot
runPermutations
Calculate observed and permutation p-values for SNPs
single.marker.test
Single SNP test
snp.list
List to describe the genotype data

Files in this package

ARTP
ARTP/inst
ARTP/inst/sampleData
ARTP/inst/sampleData/gene_SNP_data.txt
ARTP/inst/sampleData/geno_data.txt
ARTP/inst/sampleData/perm_pvalues.txt
ARTP/inst/sampleData/obs_pvalues.txt
ARTP/inst/sampleData/pheno_data.txt
ARTP/inst/doc
ARTP/inst/doc/vignette.Rnw
ARTP/inst/doc/vignette.pdf
ARTP/inst/doc/vignette.R
ARTP/src
ARTP/src/code.c
ARTP/NAMESPACE
ARTP/NEWS
ARTP/data
ARTP/data/perm_pvalues.txt.gz
ARTP/data/pheno_data.txt.gz
ARTP/data/gene_SNP_data.txt.gz
ARTP/data/geno_data.rda
ARTP/data/obs_pvalues.txt.gz
ARTP/R
ARTP/R/wga_read.R
ARTP/R/combineBypathway_Kai_C.R
ARTP/R/wga.R
ARTP/R/wga_stat.R
ARTP/R/wga_glu.R
ARTP/R/wga_combine.R
ARTP/R/wga_permReg.R
ARTP/R/wga_util.R
ARTP/R/wga_plot.R
ARTP/vignettes
ARTP/vignettes/vignette.Rnw
ARTP/MD5
ARTP/build
ARTP/build/vignette.rds
ARTP/DESCRIPTION
ARTP/man
ARTP/man/snp.list.Rd
ARTP/man/obs_pvalues.Rd
ARTP/man/gene.list.Rd
ARTP/man/ARTP.Rd
ARTP/man/runPermutations.Rd
ARTP/man/single.marker.test.Rd
ARTP/man/pheno_data.Rd
ARTP/man/gene_SNP_data.Rd
ARTP/man/pheno.list.Rd
ARTP/man/perm_pvalues.Rd
ARTP/man/geno_data.Rd
ARTP/man/plot_genes.Rd
ARTP/man/ARTP_pathway.Rd