R: Function to compute the endoPredict signature as published by...
endoPredict
R Documentation
Function to compute the endoPredict signature as published by Filipits et al 2011
Description
This function computes signature scores and risk classifications from gene expression values following the algorithm used for the endoPredict signature as published by Filipits et al 2011.
Matrix of gene expressions with samples in rows and probes in columns, dimnames being properly defined.
annot
Matrix of annotations with at least one column named "EntrezGene.ID", dimnames being properly defined.
do.mapping
TRUE if the mapping through Entrez Gene ids must be performed (in case of ambiguities, the most variant probe is kept for each gene), FALSE otherwise. Note that for Affymetrix HGU datasets, the mapping is not necessary.
mapping
Matrix with columns "EntrezGene.ID" and "probe" used to force the mapping such that the probes are not selected based on their variance.
verbose
TRUE to print informative messages, FALSE otherwise.
Details
The function works best if data have been noralized with MAS5.
Note that for Affymetrix HGU datasets, the mapping is not necessary.
Value
score
Continuous signature scores
risk
Binary risk classification, 1 being high risk and 0 being low risk.
mapping
Mapping used if necessary.
probe
If mapping is performed, this matrix contains the correspondence between the gene list (aka signature) and gene expression data.
Author(s)
Benjamin Haibe-Kains
References
ilipits, M., Rudas, M., Jakesz, R., Dubsky, P., Fitzal, F., Singer, C. F., et al. (2011). "A new molecular predictor of distant recurrence in ER-positive, HER2-negative breast cancer adds independent information to conventional clinical risk factors." Clinical Cancer Research, 17(18):6012–6020.
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)
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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/endoPredict.Rd_%03d_medium.png", width=480, height=480)
> ### Name: endoPredict
> ### Title: Function to compute the endoPredict signature as published by
> ### Filipits et al 2011
> ### Aliases: endoPredict
> ### Keywords: prognosis
>
> ### ** Examples
>
> ## load GENE70 signature
> data(sig.endoPredict)
> ## load NKI dataset
> data(vdxs)
> ## compute relapse score
> rs.vdxs <- endoPredict(data=data.vdxs, annot=annot.vdxs, do.mapping=FALSE)
>
>
>
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>
> dev.off()
null device
1
>