pik3cags: Function to compute the PIK3CA gene signature (PIK3CA-GS)

In bhklab/genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

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

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)

bhklab/genefu documentation built on Nov. 30, 2024, 9:03 p.m.