pik3cags {genefu} | R Documentation

## Function to compute the PIK3CA gene signature (PIK3CA-GS)

### Description

This function computes signature scores from gene expression values following the algorithm used for the PIK3CA gene signature (PIK3CA-GS).

### Usage

    pik3cags(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.
`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.

### Value

Vector of signature scores for PIK3CA-GS

### Author(s)

Benjamin Haibe-Kains

### References

Loi S, Haibe-Kains B, Majjaj S, Lallemand F, Durbecq V, Larsimont D, Gonzalez-Angulo AM, Pusztai L, Symmans FW, Bardelli A, Ellis P, Tutt AN, Gillett CE, Hennessy BT., Mills GB, Phillips WA, Piccart MJ, Speed TP, McArthur GA, Sotiriou C (2010) "PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor-positive breast cancer", Proceedings of the National Academy of Sciences, 107(22):10208–10213

### See Also

`gene76`

### Examples

    ## load GGI signature
    data(sig.pik3cags)
    ## load NKI dataset
    data(nkis)
    ## compute relapse score
    pik3cags.nkis <- pik3cags(data=data.nkis, annot=annot.nkis, do.mapping=TRUE)
    head(pik3cags.nkis)

[Package genefu version 2.12.0 Index]