dataFarkas: Contains three R-objects, including the data and the binary...

In GRridge: Better prediction by use of co-data: Adaptive group-regularized ridge regression

Description

The three objects are: datcenFarkas: methylation data for cervix samples (arcsine-transformed beta values); respFarkas: binary response;and CpGannFarkas: annotation of probes according to location

Format

• datcenFarkas: data frame [1:40000,1:37]

• respfarkas: Factor w/ 2 levels "Normal","Precursor"

• CpGannFarkas: Factor w/ 6 levels "CpG-Island", "North-Shelf", "South-Shelf", "North-Shore", "South-Shore", "Distant"

Details

This data is used for illustration in the statistical paper below.

Value

Three R objects, i.e. a matrix contains methylation data, a vector contains binary responses and an annotation matrix.

Source

Farkas, S. et al. (2013). Genome-wide DNA methylation assay reveals novel candidate biomarker genes in cervical cancer. Epigenetics, 8, 1213.

References

Mark van de Wiel, Tonje Lien, Wina Verlaat, Wessel van Wieringen, Saskia Wilting. (2016). Better prediction by use of co-data: adaptive group-regularized ridge regression. Statistics in Medicine, 35(3), 368-81.

Examples

data(dataFarkas)

Example output

Loading required package: penalized
Loading required package: survival
Welcome to penalized. For extended examples, see vignette("penalized").
Loading required package: Iso
Iso 0.0-17
Loading required package: GSEABase
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 object is masked from 'package:penalized':

    as.data.frame

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

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

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

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

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

    addNode

Warning messages:
1: replacing previous import 'stats::xtabs' by 'BiocGenerics::xtabs' when loading 'GRridge' 
2: replacing previous import 'stats::sd' by 'BiocGenerics::sd' when loading 'GRridge' 
3: replacing previous import 'stats::mad' by 'BiocGenerics::mad' when loading 'GRridge' 
4: replacing previous import 'stats::IQR' by 'BiocGenerics::IQR' when loading 'GRridge' 
5: replacing previous import 'GSEABase::intersect' by 'BiocGenerics::intersect' when loading 'GRridge' 
6: replacing previous import 'penalized::as.data.frame' by 'BiocGenerics::as.data.frame' when loading 'GRridge' 
7: replacing previous import 'GSEABase::setdiff' by 'BiocGenerics::setdiff' when loading 'GRridge' 
8: replacing previous import 'stats::var' by 'BiocGenerics::var' when loading 'GRridge' 

GRridge documentation built on Nov. 8, 2020, 5:47 p.m.