Last data update: 2014.03.03

R: Classify using the Lasso
lassoClassR Documentation

Classify using the Lasso

Description

Classify using the Lasso algorithm as implemented in the glmnet package

Usage

lassoClass(object, groups)

Arguments

object

object containing the expression measurements; currently the only method supported is one for ExpressionSet objects

groups

character string indicating the column containing the class membership

Value

object of class glmnet

Author(s)

Willem Talloen

References

Goehlmann, H. and W. Talloen (2009). Gene Expression Studies Using Affymetrix Microarrays, Chapman & Hall/CRC, pp. 183, 205 and 212.

See Also

glmnet

Examples


if (require(ALL)){
  data(ALL, package = "ALL")
  ALL <- addGeneInfo(ALL)
  ALL$BTtype <- as.factor(substr(ALL$BT,0,1))

  resultLasso <- lassoClass(object = ALL, groups = "BTtype")
  plot(resultLasso, label = TRUE,
    main = "Lasso coefficients in relation to degree of
  penalization.")
  featResultLasso <- topTable(resultLasso, n = 15)
}

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(a4Classif)
Loading required package: a4Core
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-5

Loading required package: a4Preproc
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    colMeans, colSums, expand, rowMeans, rowSums

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: XML
Loading required package: cluster
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess

Loading required package: pamr
Loading required package: survival
Loading required package: varSelRF
Loading required package: randomForest
randomForest 4.6-12
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

The following object is masked from 'package:Biobase':

    combine

The following object is masked from 'package:BiocGenerics':

    combine


a4Classif version 1.20.0

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/a4Classif/lassoClass.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lassoClass
> ### Title: Classify using the Lasso
> ### Aliases: lassoClass
> ### Keywords: models
> 
> ### ** Examples
> 
> 
> if (require(ALL)){
+   data(ALL, package = "ALL")
+   ALL <- addGeneInfo(ALL)
+   ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
+ 
+   resultLasso <- lassoClass(object = ALL, groups = "BTtype")
+   plot(resultLasso, label = TRUE,
+     main = "Lasso coefficients in relation to degree of
+   penalization.")
+   featResultLasso <- topTable(resultLasso, n = 15)
+ }
Loading required package: ALL
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db


> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>