R: Function to compute the Gene Expression progNostic Index...
genius
R Documentation
Function to compute the Gene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010
Description
This function computes the Gene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010. Subtype-specific risk scores are computed for each subtype signature separately and an overall risk score is computed by combining these scores with the posterior probability to belong to each of the breast cancer molecular subtypes.
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.
mapping
Matrix with columns "EntrezGene.ID" and "probe" used to force the mapping such that the probes are not selected based on their variance.
do.scale
TRUE if the ESR1, ERBB2 and AURKA (module) scores must be rescaled (see rescale), FALSE otherwise.
Value
GENIUSM1
Risk score from the ER-/HER2- subtype signature in GENIUS model.
GENIUSM2
Risk score from the HER2+ subtype signature in GENIUS model.
GENIUSM3
Risk score from the ER+/HER2- subtype signature in GENIUS model.
score
Overall risk prediction as computed by the GENIUS model.
Author(s)
Benjamin Haibe-Kains
References
Haibe-Kains B, Desmedt C, Rothe F, Sotiriou C and Bontempi G (2010) "A fuzzy gene expression-based computational approach improves breast cancer prognostication", Genome Biology, 11(2):R18
See Also
subtype.cluster.predict,sig.score
Examples
## load NKI dataset
data(nkis)
## compute GENIUS risk scores based on GENIUS model fitted on VDX dataset
genius.nkis <- genius(data=data.nkis, annot=annot.nkis, do.mapping=TRUE)
str(genius.nkis)
## the performance of GENIUS overall risk score predictions are not optimal
## since only part of the NKI dataset was used
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/genius.Rd_%03d_medium.png", width=480, height=480)
> ### Name: genius
> ### Title: Function to compute the Gene Expression progNostic Index Using
> ### Subtypes (GENIUS) as published by Haibe-Kains et al. 2010
> ### Aliases: genius
> ### Keywords: prognosis
>
> ### ** Examples
>
> ## load NKI dataset
> data(nkis)
> ## compute GENIUS risk scores based on GENIUS model fitted on VDX dataset
> genius.nkis <- genius(data=data.nkis, annot=annot.nkis, do.mapping=TRUE)
> str(genius.nkis)
List of 4
$ GENIUSM1: atomic [1:150] 0.791 -0.148 -0.205 0.386 0.465 ...
..- attr(*, "q1")= Named num -0.101
.. ..- attr(*, "names")= chr "2.5%"
..- attr(*, "q2")= Named num 0.0953
.. ..- attr(*, "names")= chr "97.5%"
$ GENIUSM2: atomic [1:150] 0.493 -0.762 0.515 0.434 0.358 ...
..- attr(*, "q1")= Named num -0.414
.. ..- attr(*, "names")= chr "2.5%"
..- attr(*, "q2")= Named num 0.227
.. ..- attr(*, "names")= chr "97.5%"
$ GENIUSM3: atomic [1:150] -0.586 0.884 -0.178 -0.937 -0.927 ...
..- attr(*, "q1")= Named num -0.148
.. ..- attr(*, "names")= chr "2.5%"
..- attr(*, "q2")= Named num 0.188
.. ..- attr(*, "names")= chr "97.5%"
$ score : Named num [1:150] -0.586 0.884 -0.178 -0.936 -0.925 ...
..- attr(*, "names")= chr [1:150] "NKI_123" "NKI_327" "NKI_291" "NKI_370" ...
> ## the performance of GENIUS overall risk score predictions are not optimal
> ## since only part of the NKI dataset was used
>
>
>
>
>
> dev.off()
null device
1
>