doMetagene: Creates metagroups of genes
In cbg-ethz/TiMEx: Finding Mutually Exclusive Groups of Alterations in Cancer Datasets

Description Usage Arguments Details Value Author(s) References See Also Examples

doMetagene collapses genes with identical alteration patterns across patients into metagroups. It returns a new matrix with the collapsed genes, as well as the members of the metagroups.

1	doMetagene(mat)

mat

binary alteration matrix, with rows representing patients and columns representing genes

It is recommended to run this function on the input binary matrix before applying TiMEx, because genes with identical alteration patterns across patients will otherwise be indistinguishable.

Note that in the datasets provided in this package, the genes have already been collapsed into metagroups.

List consisting of:

newMat the collapsed input binary matrix, with metagenes instead of genes.
groups list of metagenes, with as many elements as input genes which had an identical alteration pattern with at least one other input gene.

Simona Cristea, scristea@jimmy.harvard.edu

Constantinescu et al.: TiMEx: A Waiting Time Model for Mutually Exclusive Cancer Alterations. Bioinformatics (2015).

ovarianGroups, breastGroups for examples of metagroups in large cancer datasets.

# Simulate genes and extract groups
simGenes<-simulateGenes(c(0.5,1,0.3),0.8,4000)
genes<-cbind(simGenes$genes,simGenes$genes)
genesNew<-doMetagene(genes)

# In the datasets provided in this package, the genes have already been 
# collapsed into metagroups, hence the new matrix will be identical to the 
# old one.
data(ovarian)
ovarianNew<-doMetagene(ovarian)