ggi {genefu} | R Documentation

## Function to compute the raw and scaled Gene expression Grade Index (GGI)

### Description

This function computes signature scores and risk classifications from gene expression values following the algorithm used for the Gene expression Grade Index (GGI).

### Usage

    ggi(data, annot, do.mapping = FALSE, mapping, hg, 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.
`mapping` | Matrix with columns "EntrezGene.ID" and "probe" used to force the mapping such that the probes are not selected based on their variance.
`hg` | Vector containing the histological grade (HG) status of breast cancer patients in the dataset.
`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

Sotiriou C, Wirapati P, Loi S, Harris A, Bergh J, Smeds J, Farmer P, Praz V, Haibe-Kains B, Lallemand F, Buyse M, Piccart MJ and Delorenzi M (2006) "Gene expression profiling in breast cancer: Understanding the molecular basis of histologic grade to improve prognosis", Journal of National Cancer Institute, 98:262–272

### See Also

`gene76`

### Examples

    ## load GGI signature
    data(sig.ggi)
    ## load NKI dataset
    data(nkis)
    ## compute relapse score
    ggi.nkis <- ggi(data=data.nkis, annot=annot.nkis, do.mapping=TRUE,
      hg=demo.nkis[ ,"grade"])
    table(ggi.nkis$risk)

[Package genefu version 2.20.0 Index]