plmDE: Additive partially linear models for differential gene expression analysis
Version 1.0

A set of tools for identifying genes whose differential expression is associated with measurements of other covariates on a continuous scale. These methods rely on generalized additive partially linear models which can be fitted efficiently using a B-spline basis approximation. Still under development: methods for interfacing with objects extending the eSet class and a function to pass linear models in edgeR and DEseq format.

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AuthorJonas Mueller
Date of publication2012-05-09 04:06:58
MaintainerJonas <jonasmueller303@hotmail.com>
LicenseGPL (>= 2)
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("plmDE")

Man pages

fitBspline: Compute B-Spline Basis for Data
fitGAPLM: Fit a Generalized Additive Partially Linear Model on Gene...
head.DEresults: Preview of Data in 'DEresults' object
head.plmDE: Preview of 'plmDE' object
histDEresults: Create a Histogram of P-values
info: Information about an Object
info.plmDE: Obtain Information about 'plmDE' object
limmaPLM: Adapt Additive Partially Linear Models for Testing via...
mostDE: Find Genes with the Most Evidence for Differential Expression
plmDEmodel: Constructor for objects of type 'plmDE'
plmDEmodel.default: Creates a class to hold Expression Data and Other...
plmDE-package: Generalized Additive Partially Linear Models for Gene...
plot.DEresults: Plot Fit of 'DEresults' Model

Functions

fitBspline Man page Source code
fitGAPLM Man page Source code
head.DEresults Man page Source code
head.plmDE Man page Source code
hist.DEresults Man page Source code
info Man page Source code
info.plmDE Man page Source code
limmaPLM Man page Source code
mostDE Man page Source code
plmDE Man page
plmDE-package Man page
plmDEmodel Man page Source code
plmDEmodel.default Man page Source code
plot.DEresults Man page Source code

Files

MD5
R
R/plot.DEresults.R
R/plmDEmodel.R
R/plmDEmodel.default.R
R/mostDE.R
R/limmaPLM.R
R/info.R
R/info.plmDE.R
R/hist.DEresults.R
R/head.plmDE.R
R/head.DEresults.R
R/fitGAPLM.R
R/fitBspline.R
NAMESPACE
man
man/plot.DEresults.Rd
man/plmDEmodel.Rd
man/plmDEmodel.default.Rd
man/plmDE-package.Rd
man/mostDE.Rd
man/limmaPLM.Rd
man/info.Rd
man/info.plmDE.Rd
man/histDEresults.Rd
man/head.plmDE.Rd
man/head.DEresults.Rd
man/fitGAPLM.Rd
man/fitBspline.Rd
DESCRIPTION
plmDE documentation built on May 19, 2017, 4:32 p.m.