plmDE: Additive partially linear models for differential gene expression analysis

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.

Author
Jonas Mueller
Date of publication
2012-05-09 04:06:58
Maintainer
Jonas <jonasmueller303@hotmail.com>
License
GPL (>= 2)
Version
1.0

View on CRAN

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

Files in this package

plmDE
plmDE/MD5
plmDE/R
plmDE/R/plot.DEresults.R
plmDE/R/plmDEmodel.R
plmDE/R/plmDEmodel.default.R
plmDE/R/mostDE.R
plmDE/R/limmaPLM.R
plmDE/R/info.R
plmDE/R/info.plmDE.R
plmDE/R/hist.DEresults.R
plmDE/R/head.plmDE.R
plmDE/R/head.DEresults.R
plmDE/R/fitGAPLM.R
plmDE/R/fitBspline.R
plmDE/NAMESPACE
plmDE/man
plmDE/man/plot.DEresults.Rd
plmDE/man/plmDEmodel.Rd
plmDE/man/plmDEmodel.default.Rd
plmDE/man/plmDE-package.Rd
plmDE/man/mostDE.Rd
plmDE/man/limmaPLM.Rd
plmDE/man/info.Rd
plmDE/man/info.plmDE.Rd
plmDE/man/histDEresults.Rd
plmDE/man/head.plmDE.Rd
plmDE/man/head.DEresults.Rd
plmDE/man/fitGAPLM.Rd
plmDE/man/fitBspline.Rd
plmDE/DESCRIPTION