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

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

AuthorBenoit Liquet, Therese Truong
Date of publication2013-12-30 07:44:39
MaintainerBenoit Liquet <benoit.liquet@isped.u-bordeaux2.fr>
LicenseGPL (>= 2.0)
Version0.9

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...

Functions

ARTP.GE Man page
compute.p.snp.obs Man page
data.pathway Man page
data.pathway.surv Man page
data.pige Man page
data.surv Man page
data.to.list.gene.snp Man page
data.to.PIGE Man page
list.gene.snp Man page
list.gene.snp.surv Man page
LR.cont Man page
LR.cont.surv Man page
LR.inter.cat Man page
LR.inter.cat.surv Man page
LR.inter.cont Man page
LR.inter.cont.surv Man page
permutation.snp Man page
permutation.wrapper.cat.inter Man page
permutation.wrapper.cat.inter.Y.and.X Man page
permutation.wrapper.cont Man page
permutation.wrapper.cont.inter Man page
permutation.wrapper.cont.inter.Y.and.X Man page
permutation.wrapper.cont.Y.and.X Man page
PIGE Man page
PIGE-package Man page
snp.gene.select Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.