plsgenomics: PLS Analyses for Genomics
Version 1.3-1

Routines for PLS-based genomic analyses, implementing PLS methods for classification with microarray data and prediction of transcription factor activities from combined ChIP-chip analysis. The >=1.2-1 versions include two new classification methods for microarray data: GSIM and Ridge PLS. The >=1.3 versions includes a new classification method combining variable selection and compression in logistic regression context: RIRLS-SPLS; and an adaptive version of the sparse PLS.

AuthorAnne-Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>, Ghislain Durif <ghislain.durif@univ-lyon1.fr>, Sophie Lambert-Lacroix <Sophie.Lambert@imag.fr>, Julie Peyre <Julie.Peyre@imag.fr>, and Korbinian Strimmer <strimmer@uni-leipzig.de>.
Date of publication2015-05-11 14:57:01
MaintainerGhislain Durif <ghislain.durif@univ-lyon1.fr>
LicenseGPL (>= 2)
Version1.3-1
URL http://cran.r-project.org/web/packages/plsgenomics/index.html
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("plsgenomics", repos="http://R-Forge.R-project.org")

Popular man pages

Colon: Gene expression data from Alon et al. (1999)
leukemia: Gene expression data from Golub et al. (1999)
rirls.spls.tune: Tuning parameters (ncomp, lambda.l1, lambda.ridge) for Ridge...
spls.adapt: Classification by Ridge Iteratively Reweighted Least Squares...
SRBCT: Gene expression data from Khan et al. (2001)
TFA.estimate: Prediction of Transcription Factor Activities using PLS
variable.selection: Variable selection using the PLS weights
See all...

All man pages Function index File listing

Man pages

Colon: Gene expression data from Alon et al. (1999)
Ecoli: Ecoli gene expression and connectivity data from Kao et al....
gsim: GSIM for binary data
gsim.cv: Determination of the ridge regularization parameter and the...
leukemia: Gene expression data from Golub et al. (1999)
mgsim: GSIM for categorical data
mgsim.cv: Determination of the ridge regularization parameter and the...
mrpls: Ridge Partial Least Square for categorical data
mrpls.cv: Determination of the ridge regularization parameter and the...
plsgenomics-internal: Internal plsgenomics Functions
pls.lda: Classification with PLS Dimension Reduction and Linear...
pls.lda.cv: Determination of the number of latent components to be used...
pls.regression: Multivariate Partial Least Squares Regression
pls.regression.cv: Determination of the number of latent components to be used...
preprocess: preprocess for microarray data
rirls.spls: Classification by Ridge Iteratively Reweighted Least Squares...
rirls.spls.tune: Tuning parameters (ncomp, lambda.l1, lambda.ridge) for Ridge...
rpls: Ridge Partial Least Square for binary data
rpls.cv: Determination of the ridge regularization parameter and the...
sample.bin: Generates design matrix X with correlated block of covariates...
sample.cont: Generates design matrix X with correlated block of covariates...
spls.adapt: Classification by Ridge Iteratively Reweighted Least Squares...
spls.adapt.tune: Tuning parameters (ncomp, lambda.l1) for Adaptive Sparse PLS...
SRBCT: Gene expression data from Khan et al. (2001)
TFA.estimate: Prediction of Transcription Factor Activities using PLS
variable.selection: Variable selection using the PLS weights

Functions

Files

DESCRIPTION
LICENCE.note
NAMESPACE
R
R/TFA.estimate.R
R/gsim.R
R/gsim.aux.R
R/gsim.cv.R
R/hplugin.R
R/mgsim.R
R/mgsim.cv.R
R/mgsimaux.R
R/mrpls.R
R/mrpls.cv.R
R/mrplsaux.R
R/mwirrls.R
R/pls.lda.R
R/pls.lda.cv.R
R/pls.regression.R
R/pls.regression.cv.R
R/preprocess.R
R/rirls.spls.R
R/rirls.spls.aux.R
R/rirls.spls.tune.R
R/rpls.R
R/rpls.cv.R
R/rplsaux.R
R/sample.bin.R
R/sample.cont.R
R/spls.adapt.R
R/spls.adapt.aux.R
R/spls.adapt.tune.R
R/ust.R
R/ust.adapt.R
R/variable.selection.R
R/wirrls.R
R/wpls.R
README
data
data/Colon.rda
data/Ecoli.rda
data/SRBCT.rda
data/datalist
data/leukemia.rda
man
man/Colon.Rd
man/Ecoli.Rd
man/SRBCT.Rd
man/TFA.estimate.Rd
man/gsim.Rd
man/gsim.cv.Rd
man/leukemia.Rd
man/mgsim.Rd
man/mgsim.cv.Rd
man/mrpls.Rd
man/mrpls.cv.Rd
man/pls.lda.Rd
man/pls.lda.cv.Rd
man/pls.regression.Rd
man/pls.regression.cv.Rd
man/plsgenomics-internal.Rd
man/preprocess.Rd
man/rirls.spls.Rd
man/rirls.spls.tune.Rd
man/rpls.Rd
man/rpls.cv.Rd
man/sample.bin.Rd
man/sample.cont.Rd
man/spls.adapt.Rd
man/spls.adapt.tune.Rd
man/variable.selection.Rd
tests
tests/plsgenomics-Ex.R
plsgenomics documentation built on May 21, 2017, 12:43 a.m.

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