ovcTCGA {genefu} | R Documentation

## Function to compute the prediction scores and risk classifications for the ovarian cancer TCGA signature

### Description

This function computes signature scores and risk classifications from gene expression values following the algorithm developed by the TCGA consortium for ovarian cancer.

### Usage

    ovcTCGA(data, annot,
    gmap = c("entrezgene", "ensembl_gene_id", "hgnc_symbol", "unigene"),
    do.mapping = FALSE, 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 one column named as gmap, dimnames being properly defined.
`gmap` | character string containing the `biomaRt` attribute to use for mapping if `do.mapping=TRUE`
`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.
`verbose` | `TRUE` to print informative messages, `FALSE` otherwise.

### 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

Bell D, Berchuck A, Birrer M et al. (2011) "Integrated genomic analyses of ovarian carcinoma", Nature, 474(7353):609–615

### See Also

`sigOvcTCGA`

### Examples

    ## load the ovcTCGA signature
    data(sigOvcTCGA)
    ## load NKI dataset
    data(nkis)
    colnames(annot.nkis)[is.element(colnames(annot.nkis), "EntrezGene.ID")] <- "entrezgene"
    ## compute relapse score
    ovcTCGA.nkis <- ovcTCGA(data=data.nkis, annot=annot.nkis, gmap="entrezgene", do.mapping=TRUE)
    table(ovcTCGA.nkis$risk)

[Package genefu version 2.12.0 Index]