gene76: Function to compute the Relapse Score as published by Wang et...

In genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

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

data	Matrix of gene expressions with samples in rows and probes in columns, dimnames being properly defined.
er	Vector containing the estrogen receptor (ER) status of breast cancer patients in the dataset.

Value

score	Continuous signature scores
risk	Binary risk classification, 1 being high risk and 0 being low risk.

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)

Example output

Loading required package: survcomp
Loading required package: survival
Loading required package: prodlim
Loading required package: mclust
Package 'mclust' version 5.4.2
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, sd, var, xtabs

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

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

Welcome to Bioconductor

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


 0  1 
54 96 

genefu documentation built on Jan. 28, 2021, 2:01 a.m.