pik3cags {genefu} | R Documentation |
This function computes signature scores from gene expression values following the algorithm used for the PIK3CA gene signature (PIK3CA-GS).
pik3cags(data, annot, do.mapping = FALSE, mapping, verbose = FALSE)
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 |
|
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 |
|
Vector of signature scores for PIK3CA-GS
Benjamin Haibe-Kains
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
## 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)