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.

Author | Anne-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 publication | 2015-05-11 14:57:01 |

Maintainer | Ghislain Durif <ghislain.durif@univ-lyon1.fr> |

License | GPL (>= 2) |

Version | 1.3-1 |

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

**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

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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