pipeGS: Permutation p-Value Estimation for Gene Set Tests

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" <https://searchworks.stanford.edu/view/11849351>. One of the methods also corresponds to the paper "Permutation p-value approximation via generalized Stolarsky invariance" <https://arxiv.org/abs/1603.02757>.

Author
Hera He <njheyu@gmail.com>
Date of publication
2016-11-17 01:48:16
Maintainer
Hera He <njheyu@gmail.com>
License
GPL-2
Version
0.1
URLs

View on CRAN

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.

Files in this package

pipeGS
pipeGS/NAMESPACE
pipeGS/R
pipeGS/R/saddlepoint.R
pipeGS/R/pipegs.R
pipeGS/R/nested.R
pipeGS/R/stolarsky.R
pipeGS/R/montecarlo.R
pipeGS/R/parallelexact.R
pipeGS/R/normalize.R
pipeGS/R/functiondef.R
pipeGS/R/main.R
pipeGS/MD5
pipeGS/DESCRIPTION
pipeGS/man
pipeGS/man/get.phat.quadratic.Rd
pipeGS/man/get.phat.linear.Rd
pipeGS/man/pipegs.Rd