ROIq: Function that will assign the AIPS models to a gene...

In meoyo/AIPS: AIPS : Absolute Inference of Patient Signatures

Description

Given a gene expression matrix D where rows correspond to genes and columns to samples, and a gene set, this function will compute the ROIq assignements (low, independent, or high) associated to samples in matrix D.

Usage

ROIq (D,genename,gene.set,n=1000,q=0.95)

Arguments

D	A matrix D of gene expression. Rows are genes and columns are samples (tumor from breast cancer patients).
genename	A character vector corresponding to the genenames of the genes of matrix D. Expect length(genename) == nrow(D)
gene.set	A list element (list(up=,down=)) corresponding to the genes in the gene signature. The up-regulated genes should be set in "up" and the down-regulated genes should be set in "down".
n	Number of random sampling necessary to define the region of independence.
q	The fraction of random sampling contained within the region of independence.

Details

This function will compute the Region Of Independence at quantile q (ROIq) descibe in Paquet et al. Given a gene expression dataset, a list of gene names, and a gene signature the function will identify the region of independence and will return assignments associated to the patients given the gene signatures. The assignment could be low, independent, or high in function of how strongly the patients are associated to the gene signature.

Value

cl	Gene signature activation identified by AIPS. It could be either "low", "random/independent", or "high".

Author(s)

Eric R. Paquet ([e-mail]), Ali Tofigh ([e-mail]), Robert Lesurf ([e-mail])

References

Paquet ER, Hallett MT. J Natl Cancer Inst. 2014 Dec 4;107(1):357

See Also

mcgill.gq

Examples

## Load the McGill dataset used in the paper
data(mcgill.gq)
data(aips.models)

## Get one esr1 (estrogen) gene signature
esr1.gs = aips.models[[1706]]$gs.bresat

## Assigned the ROI95 on McGill dataset using the esr1 gene signature
mcgill.ROI95.esr1.gs <- ROIq (mcgill.gq$D,
                              mcgill.gq$EntrezID,
                              list(up=esr1.gs$ENTREZ$up,down=esr1.gs$ENTREZ$down))

## Print a summary of all the assignments
table(mcgill.ROI95.esr1.gs$cl)

meoyo/AIPS documentation built on May 22, 2019, 6:51 p.m.