Function to compute the Relapse Score as published by Wang et al. 2005

Description

This function computes signature scores and risk classifications from gene expression values following the algorithm used for the Relapse Score (GENE76) as published by Wang et al. 2005.

Usage

gene76(data, er)

Arguments

Value

Author(s)

Benjamin Haibe-Kains

References

Y. Wang and J. G. Klijn and Y. Zhang and A. M. Sieuwerts and M. P. Look and F. Yang and D. Talantov and M. Timmermans and M. E. Meijer-van Gelder and J. Yu and T. Jatkoe and E. M. Berns and D. Atkins and J. A. Foekens (2005) "Gene-Expression Profiles to Predict Distant Metastasis of Lymph-Node-Negative Primary Breast Cancer", Lancet, 365(9460):671–679.

See Also

ggi

Examples

## load GENE76 signature
data(sig.gene76)
## load VDX dataset
data(vdxs)
## compute relapse score
rs.vdxs <- gene76(data=data.vdxs, er=demo.vdxs[ ,"er"])
table(rs.vdxs$risk)

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(genefu)
Loading required package: survcomp
Loading required package: survival
Loading required package: prodlim
Loading required package: mclust
Package 'mclust' version 5.2
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: limma
Loading required package: biomaRt
Loading required package: iC10
Loading required package: pamr
Loading required package: cluster
Loading required package: iC10TrainingData
Loading required package: AIMS
Loading required package: e1071
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 object is masked from 'package:limma':

    plotMA

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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/genefu/gene76.Rd_%03d_medium.png", width=480, height=480)
> ### Name: gene76
> ### Title: Function to compute the Relapse Score as published by Wang et
> ###   al. 2005
> ### Aliases: gene76
> ### Keywords: prognosis
> 
> ### ** Examples
> 
> ## load GENE76 signature
> data(sig.gene76)
> ## load VDX dataset
> data(vdxs)
> ## compute relapse score
> rs.vdxs <- gene76(data=data.vdxs, er=demo.vdxs[ ,"er"])
> table(rs.vdxs$risk)

 0  1 
54 96 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>