endoPredict: Function to compute the endoPredict signature as published by...

Description Usage Arguments Details Value Author(s) References Examples

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.

Usage

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endoPredict(data, annot, do.mapping = FALSE, mapping, verbose = FALSE)

Arguments

data

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.

Examples

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## 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)

Example output

Loading required package: survcomp
Loading required package: survival
Loading required package: prodlim
Loading required package: mclust
Package 'mclust' version 5.4.7
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: impute
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:BiocGenericsThe following objects are masked frompackage:parallel:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked frompackage:limma:

    plotMA

The following objects are masked frompackage:stats:

    IQR, mad, sd, var, xtabs

The following objects are masked frompackage:base:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, 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")'.

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