produceTablesSignifGroups: Produces tables with groups
In cbg-ethz/TiMEx: Finding Mutually Exclusive Groups of Alterations in Cancer Datasets

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

produceTablesSignifGroups produces tables with the significant groups. These tables include the names of the genes part of the groups, their respective frequency in the dataset, and the mu and corrected pvalue corresponding to each group.

1	produceTablesSignifGroups(signifGroups, mat, noToShow)

`signifGroups`	result structure with the significant groups, as returned by either `TiMEx` or `findSignifCliques`
`mat`	binary alteration matrix, with rows representing patients and columns representing genes
`noToShow`	maximum number of groups to include in the table. Default is 30.

This function summarizes information on the mutually exclusive groups identified by TiMEx in a dataset, as tables.

list with as many elements as lengths of the identified mutually exclusive groups, containing tables with the significant groups for each size. Each list of this type further has two elements, fdr and bonf, corresponding to different multiple testing correction methods. Each element is a matrix, in which rows represent significantly mutually exclusive groups.

Simona Cristea, scristea@jimmy.harvard.edu

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

the wrapper function TiMEx for identifying mutually exclusive groups in a binary dataset with the TiMEx model.

# Produce tables on the output of TiMEx on the ovarian cancer dataset
data(ovarian)
data(ovarianOutput)
ovarianTables<-produceTablesSignifGroups(ovarianOutput,ovarian)