plsgenomics: PLS Analyses for Genomics
Version 1.3-2

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.

Browse man pages Browse package API and functions Browse package files

AuthorAnne-Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>, Ghislain Durif <gd.dev@libertymail.net>, Sophie Lambert-Lacroix <Sophie.Lambert@imag.fr>, Julie Peyre <Julie.Peyre@imag.fr>, and Korbinian Strimmer <strimmer@uni-leipzig.de>.
Date of publication2017-05-02 16:39:12 UTC
MaintainerGhislain Durif <gd.dev@libertymail.net>
LicenseGPL (>= 2)
Version1.3-2
URL https://CRAN.R-project.org/package=plsgenomics
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("plsgenomics")

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

Colon Man page
Ecoli Man page
SRBCT Man page
TFA.estimate Man page Source code
gsim Man page Source code
gsim.aux Man page Source code
gsim.cv Man page Source code
hplugin Man page Source code
leukemia Man page
mgsim Man page Source code
mgsim.cv Man page Source code
mgsimaux Man page Source code
mrpls Man page Source code
mrpls.cv Man page Source code
mrplsaux Man page Source code
mwirrls Man page Source code
pls.lda Man page Source code
pls.lda.cv Man page Source code
pls.lda.sample Man page Source code
pls.regression Man page Source code
pls.regression.cv Man page Source code
pls.regression.sample Man page Source code
preprocess Man page Source code
rirls.spls Man page Source code
rirls.spls.aux Man page Source code
rirls.spls.tune Man page Source code
rpls Man page Source code
rpls.cv Man page Source code
rplsaux Man page Source code
sample.bin Man page Source code
sample.cont Man page Source code
spls.adapt Man page Source code
spls.adapt.aux Man page Source code
spls.adapt.tune Man page Source code
standard.simpls Man page Source code
transformy Man page Source code
unitr.simpls Man page Source code
ust Man page Source code
ust.adapt Man page Source code
variable.selection Man page Source code
wirrls Man page Source code
wpls Man page Source code

Files

tests
tests/plsgenomics-Ex.R
NAMESPACE
data
data/leukemia.rda
data/Ecoli.rda
data/SRBCT.rda
data/datalist
data/Colon.rda
R
R/rirls.spls.R
R/TFA.estimate.R
R/pls.lda.R
R/pls.regression.cv.R
R/ust.adapt.R
R/rirls.spls.aux.R
R/pls.regression.R
R/gsim.R
R/mgsim.cv.R
R/preprocess.R
R/sample.cont.R
R/hplugin.R
R/mrpls.R
R/variable.selection.R
R/sample.bin.R
R/rirls.spls.tune.R
R/wpls.R
R/ust.R
R/spls.adapt.tune.R
R/rplsaux.R
R/mgsimaux.R
R/rpls.R
R/mgsim.R
R/wirrls.R
R/mrpls.cv.R
R/rpls.cv.R
R/mrplsaux.R
R/pls.lda.cv.R
R/gsim.aux.R
R/mwirrls.R
R/spls.adapt.aux.R
R/gsim.cv.R
R/spls.adapt.R
MD5
README
DESCRIPTION
man
man/preprocess.Rd
man/Colon.Rd
man/mrpls.Rd
man/TFA.estimate.Rd
man/leukemia.Rd
man/mrpls.cv.Rd
man/mgsim.cv.Rd
man/spls.adapt.tune.Rd
man/sample.bin.Rd
man/pls.lda.cv.Rd
man/pls.regression.Rd
man/gsim.Rd
man/rirls.spls.tune.Rd
man/mgsim.Rd
man/plsgenomics-internal.Rd
man/pls.lda.Rd
man/gsim.cv.Rd
man/rpls.cv.Rd
man/Ecoli.Rd
man/rirls.spls.Rd
man/variable.selection.Rd
man/spls.adapt.Rd
man/sample.cont.Rd
man/pls.regression.cv.Rd
man/SRBCT.Rd
man/rpls.Rd
LICENCE.note
plsgenomics documentation built on May 20, 2017, 12:47 a.m.