pipeGS: Permutation p-Value Estimation for Gene Set Tests
Version 0.1

Code for various permutation p-values estimation methods for gene set test. The description of corresponding methods can be found in the dissertation of Yu He(2016) "Efficient permutation P-value estimation for gene set tests" . One of the methods also corresponds to the paper "Permutation p-value approximation via generalized Stolarsky invariance" .

AuthorHera He <njheyu@gmail.com>
Date of publication2016-11-17 01:48:16
MaintainerHera He <njheyu@gmail.com>
LicenseGPL-2
Version0.1
URL https://searchworks.stanford.edu/view/11849351 https://arxiv.org/abs/1603.02757
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("pipeGS")

Popular man pages

get.phat.linear: Get the pvalue for the linear statistic
get.phat.quadratic: Get the pvalue for the quadratic statistic
pipegs: pvalue approximation with stolarsky invariance principal.
See all...

All man pages Function index File listing

Man pages

get.phat.linear: Get the pvalue for the linear statistic
get.phat.quadratic: Get the pvalue for the quadratic statistic
pipegs: pvalue approximation with stolarsky invariance principal.

Functions

dp.large Source code
dp.small Source code
dp.small.reduced Source code
dq.large Source code
dq.small Source code
dq.small.reduced Source code
get.a Source code
get.exact Source code
get.exact.par Source code
get.exact.regular Source code
get.exact.saddle Source code
get.indicator.reduced Source code
get.indicator.regular Source code
get.mapping Source code
get.mc Source code
get.mixture.param Source code
get.phat.linear Man page Source code
get.phat.quadratic Man page Source code
get.rho.hat Source code
get.saddle Source code
get.stolarsky Source code
matrix.power Source code
nested.estimation Source code
nested.estimation.linear Source code
next.comb Source code
normalize Source code
pipegs Man page
pipegs-package Man page
plain.mc.linear Source code
plain.mc.quadratic Source code
project.y.to.discrete Source code
rp.large Source code
rp.small Source code
rp.small.reduced Source code
rq.large Source code
rq.small Source code
rq.small.reduced Source code
rtrunc.beta Source code
rtrunc.chisq Source code
test.rtrunc.beta Source code
uniform.mcmc Source code
uniform.mcmc.linear Source code

Files

NAMESPACE
R
R/saddlepoint.R
R/pipegs.R
R/nested.R
R/stolarsky.R
R/montecarlo.R
R/parallelexact.R
R/normalize.R
R/functiondef.R
R/main.R
MD5
DESCRIPTION
man
man/get.phat.quadratic.Rd
man/get.phat.linear.Rd
man/pipegs.Rd
pipeGS documentation built on May 19, 2017, 11:16 a.m.

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