plsgenomics: PLS Analyses for Genomics

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
http://cran.r-project.org/web/packages/plsgenomics/index.html

View on R-Forge

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

Files in this package

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

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