ovcAngiogenic {genefu} | R Documentation

## Function to compute the subtype scores and risk classifications for the angiogenic molecular subtype in ovarian cancer

### Description

This function computes subtype scores and risk classifications from gene expression values following the algorithm developed by Bentink, Haibe-Kains et al. to identify the angiogenic molecular subtype in ovarian cancer.

### Usage

    ovcAngiogenic(data, annot, hgs,
    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.
`hgs` | vector of booleans with TRUE represents the ovarian cancer patients who have a high grade, late stage, serous tumor, FALSE otherwise. This is particularly important for properly rescaling the data. If `hgs` is missing, all the patients will be used to rescale the subtype score.
`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.
`subtype` | data frame reporting the subtype score, maximum likelihood classification and corresponding subtype probabilities

### Author(s)

Benjamin Haibe-Kains

### References

Bentink S, Haibe-Kains B, Risch T, Fan J-B, Hirsch MS, Holton K, Rubio R, April C, Chen J, Wickham-Garcia E, Liu J, Culhane AC, Drapkin R, Quackenbush JF, Matulonis UA (2012) "Angiogenic mRNA and microRNA Gene Expression Signature Predicts a Novel Subtype of Serous Ovarian Cancer", PloS one, 7(2):e30269

### See Also

`sigOvcAngiogenic`

### Examples

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

[Package genefu version 2.12.0 Index]