recoverAllNamesGroups: Recovers members of the metagroups

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

Description

recoverAllNameGroups recovers, from a metagroup, the names of the genes part of an identified mutually exclusive group.

Usage

recoverAllNamesGroups(groupsMeta, clGenes)

Arguments

groupsMeta	list containing groups of equivalent genes, as returned by the field groups of doMetagene
clGenes	matrix of mutually exclusive groups of same size, as gene names. This type of matrix is returned by either TiMEx or findSignifCliques, as one of the matrix elements of the genesSignif field.

Details

This function can be used if the input binary matrix contains identical events that need to be merged into metagenes using doMetagene. Running recoverAllNamesGroups provides the set of identical alterations which are part of the identified mutually exclusive groups.

In order to run this function on all the identified mutually exclusive groups as returned by TiMEx or findSignifCliques, it is necessary to run it separately on each matrix element (corresponding to different group sizes and different correction methods) of the genesSignif field in the structure returned by either TiMEx or findSignifCliques.

For example, after loading data(ovarianGroups) and data(ovarianOutput), and running

rGroups<-recoverAllNamesGroups(ovarianGroups, signifGroups$genesSignif[[3]]$bonf)

rGroups[[14]] has 3 elements (as many as genes part of the identified mutually exclusive groups). Each element is the metagroup of each of the genes part of the 14th mutually exclusive group in the input matrix signifGroups$genesSignif[[3]]$bonf. Namely, BRD4-CNA and MYC-CNA have unique alteration patterns among samples, and are alone in their metagroup, while CASC1-CNA has an identical alteration pattern with KRAS-CNA and LYRM5-CNA. The numbers below the gene names are the indices of the genes in the initial input binary matrix of patients.

Value

list with as many elements as number of identified mutually exclusive groups, i.e. number of rows in the input matrix. Each of its elements is further a list, containing, at each position, the metagroup of the genes in the initial group at that resepective position. For an example, see Details above.

Author(s)

Simona Cristea, [e-mail]

References

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

See Also

doMetagene for collapsing the genes of an input matrix with identical alteration patterns into metagroups.

Examples

data(ovarianGroups)
data(ovarianOutput)
r<-recoverAllNamesGroups(ovarianGroups,ovarianOutput$genesSignif[[3]]$bonf)

cbg-ethz/TiMEx documentation built on May 13, 2019, 1:50 p.m.