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

A list with items:

- 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.

### 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 2.24.2 Index]