plsgenomics: PLS Analyses for Genomics

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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 17:05:40
Maintainer
Ghislain Durif <ghislain.durif@univ-lyon1.fr>
License
GPL (>= 2)
Version
1.3-1
URLs

View on CRAN

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
plsgenomics/tests
plsgenomics/tests/plsgenomics-Ex.R
plsgenomics/NAMESPACE
plsgenomics/data
plsgenomics/data/leukemia.rda
plsgenomics/data/Ecoli.rda
plsgenomics/data/SRBCT.rda
plsgenomics/data/datalist
plsgenomics/data/Colon.rda
plsgenomics/R
plsgenomics/R/rirls.spls.R
plsgenomics/R/TFA.estimate.R
plsgenomics/R/pls.lda.R
plsgenomics/R/pls.regression.cv.R
plsgenomics/R/ust.adapt.R
plsgenomics/R/rirls.spls.aux.R
plsgenomics/R/pls.regression.R
plsgenomics/R/gsim.R
plsgenomics/R/mgsim.cv.R
plsgenomics/R/preprocess.R
plsgenomics/R/sample.cont.R
plsgenomics/R/hplugin.R
plsgenomics/R/mrpls.R
plsgenomics/R/variable.selection.R
plsgenomics/R/sample.bin.R
plsgenomics/R/rirls.spls.tune.R
plsgenomics/R/wpls.R
plsgenomics/R/ust.R
plsgenomics/R/spls.adapt.tune.R
plsgenomics/R/rplsaux.R
plsgenomics/R/mgsimaux.R
plsgenomics/R/rpls.R
plsgenomics/R/mgsim.R
plsgenomics/R/wirrls.R
plsgenomics/R/mrpls.cv.R
plsgenomics/R/rpls.cv.R
plsgenomics/R/mrplsaux.R
plsgenomics/R/pls.lda.cv.R
plsgenomics/R/gsim.aux.R
plsgenomics/R/mwirrls.R
plsgenomics/R/spls.adapt.aux.R
plsgenomics/R/gsim.cv.R
plsgenomics/R/spls.adapt.R
plsgenomics/MD5
plsgenomics/README
plsgenomics/DESCRIPTION
plsgenomics/man
plsgenomics/man/preprocess.Rd
plsgenomics/man/Colon.Rd
plsgenomics/man/mrpls.Rd
plsgenomics/man/TFA.estimate.Rd
plsgenomics/man/leukemia.Rd
plsgenomics/man/mrpls.cv.Rd
plsgenomics/man/mgsim.cv.Rd
plsgenomics/man/spls.adapt.tune.Rd
plsgenomics/man/sample.bin.Rd
plsgenomics/man/pls.lda.cv.Rd
plsgenomics/man/pls.regression.Rd
plsgenomics/man/gsim.Rd
plsgenomics/man/rirls.spls.tune.Rd
plsgenomics/man/mgsim.Rd
plsgenomics/man/plsgenomics-internal.Rd
plsgenomics/man/pls.lda.Rd
plsgenomics/man/gsim.cv.Rd
plsgenomics/man/rpls.cv.Rd
plsgenomics/man/Ecoli.Rd
plsgenomics/man/rirls.spls.Rd
plsgenomics/man/variable.selection.Rd
plsgenomics/man/spls.adapt.Rd
plsgenomics/man/sample.cont.Rd
plsgenomics/man/pls.regression.cv.Rd
plsgenomics/man/SRBCT.Rd
plsgenomics/man/rpls.Rd
plsgenomics/LICENCE.note