PIGE: Self contained gene set analysis for gene- and pathway-environment interaction analysis

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Extension of the ARTP package for gene- and pathway-environment interaction

Author
Benoit Liquet, Therese Truong
Date of publication
2013-12-30 07:44:39
Maintainer
Benoit Liquet <benoit.liquet@isped.u-bordeaux2.fr>
License
GPL (>= 2.0)
Version
0.9

View on CRAN

Man pages

ARTP.GE
Gene and pathway p-values using ARTP method
compute.p.snp.obs
Likelihhod ratio test (or Wald test) for an interaction term...
data.pathway
Fictive data frame corresponding to the gene x pathway...
data.pathway.surv
Fictive data frame corresponding to the gene x pathway...
data.pige
Sample data of a case-control study
data.surv
Fictive data set for sample data of a survival analysis.
data.to.list.gene.snp
Annotation gene/SNP
data.to.PIGE
Generate data for Gene- and Pathway-environment interaction
list.gene.snp
Fictive list for the case-control study example containing...
list.gene.snp.surv
Fictive list (for survival example) containing the names of...
LR.cont
Wald test for an adjusted model.
LR.cont.surv
Wald test for an adjusted model.
LR.inter.cat
Likelihhod ratio test for an interaction term
LR.inter.cat.surv
Likelihhod ratio test for an interaction term
LR.inter.cont
Wald test for an interaction term
LR.inter.cont.surv
Wald test for an interaction term
permutation.snp
Parallel computing of the Likelihhod ratio test (or Wald...
permutation.wrapper.cat.inter
Internal function used for the parallel computation on the...
permutation.wrapper.cat.inter.Y.and.X
Internal function used for the parallel computation on the...
permutation.wrapper.cont
Internal function used for the parallel computation on the...
permutation.wrapper.cont.inter
Internal function used for the parallel computation on the...
permutation.wrapper.cont.inter.Y.and.X
Internal function used for the parallel computation on the...
permutation.wrapper.cont.Y.and.X
Internal function used for the parallel computation on the...
PIGE-package
Gene and pathway p-values using the Adaptive Rank Truncated...
snp.gene.select
Fictive data frame containing the names of the gene (first...

Files in this package

PIGE
PIGE/inst
PIGE/inst/sampleData
PIGE/inst/sampleData/res-permut-surv.txt
PIGE/inst/sampleData/res-permut.txt
PIGE/inst/sampleData/res-obs-surv.txt
PIGE/inst/sampleData/snp.gene.surv.txt
PIGE/inst/sampleData/SNP-GENE-annotation.txt
PIGE/inst/sampleData/res-obs.txt
PIGE/NAMESPACE
PIGE/data
PIGE/data/data.pathway.rda
PIGE/data/data.pathway.surv.rda
PIGE/data/data.pige.rda
PIGE/data/snp.gene.select.rda
PIGE/data/data.surv.rda
PIGE/data/list.gene.snp.rda
PIGE/data/list.gene.snp.surv.rda
PIGE/R
PIGE/R/permutation.wrapper.cont.inter.Y.and.X.R
PIGE/R/LR.inter.cat.R
PIGE/R/LR.inter.cat.surv.R
PIGE/R/permutation.wrapper.cat.inter.R
PIGE/R/data.to.PIGE.R
PIGE/R/PIGE-package.R
PIGE/R/LR.cont.surv.R
PIGE/R/permutation.wrapper.cat.inter.Y.and.X.R
PIGE/R/LR.inter.cont.R
PIGE/R/data.to.list.gene.snp.R
PIGE/R/compute.p.snp.obs.R
PIGE/R/LR.inter.cont.surv.R
PIGE/R/permutation.wrapper.cont.inter.R
PIGE/R/ARTP-GE.R
PIGE/R/LR.cont.R
PIGE/R/permutation.wrapper.cont.Y.and.X.R
PIGE/R/permutation.snp.R
PIGE/R/permutation.wrapper.cont.R
PIGE/MD5
PIGE/DESCRIPTION
PIGE/man
PIGE/man/permutation.snp.Rd
PIGE/man/LR.cont.Rd
PIGE/man/list.gene.snp.surv.Rd
PIGE/man/permutation.wrapper.cat.inter.Y.and.X.Rd
PIGE/man/LR.inter.cat.surv.Rd
PIGE/man/data.to.list.gene.snp.Rd
PIGE/man/permutation.wrapper.cont.inter.Rd
PIGE/man/permutation.wrapper.cont.inter.Y.and.X.Rd
PIGE/man/LR.cont.surv.Rd
PIGE/man/permutation.wrapper.cont.Rd
PIGE/man/snp.gene.select.Rd
PIGE/man/permutation.wrapper.cont.Y.and.X.Rd
PIGE/man/data.pige.Rd
PIGE/man/data.to.PIGE.Rd
PIGE/man/PIGE-package.Rd
PIGE/man/compute.p.snp.obs.Rd
PIGE/man/LR.inter.cat.Rd
PIGE/man/LR.inter.cont.surv.Rd
PIGE/man/LR.inter.cont.Rd
PIGE/man/data.pathway.Rd
PIGE/man/permutation.wrapper.cat.inter.Rd
PIGE/man/data.surv.Rd
PIGE/man/data.pathway.surv.Rd
PIGE/man/list.gene.snp.Rd
PIGE/man/ARTP.GE.Rd