breastSubtypesOutput: Mutually exclusive groups in breast cancer subtypes

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

Description

Dataset containing the groups identified as significantly mutually exclusive by TiMEx in each of the 4 breast cancer subtypes LuminalA, LuminalB, Her2, and Basal, together with their corresponding intensities of mutual exclusivity, corrected p-values, and other information.

Format

breastSubtypesOutput is a list consisting of 4 lists, corresponding to the 4 breast subtypes. Each list further consists of:

• genesSignif list of significantly mutually exclusive groups, as gene names, sorted by corrected p-value. The list contains as many elements as identified lengths of groups. For example, genesSignif[[2]] is a list containing the gene names of the significant groups of size 2. 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 gene names of significantly mutually exclusive groups.

• idxSignif list of significantly mutually exclusive groups, as indices in the input matrix, sorted by corrected p-value. The list contains as many elements as identified lengths of groups. For example, idxSignif[[2]] is a list containing the indices of the significant groups of size 2. 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 indices of significantly mutually exclusive groups.

• pvals list of corrected significant p-values corresponding to the tested cliques, ordered ascending. The list contains as many elements as identified lengths of significant groups. For example, pvals[[2]] is a list containing the p-values of the significant maximal cliques of size 2. Each list of this type further has two elements, fdr and bonf, corresponding to different multiple testing correction methods. Each element is a vector, of length the number of significant maximal cliques of a given size.

• posSignif list of positions of the significant groups in the input list of maximal cliques, ordered ascending by corrected p-value. The list contains as many elements as identified lengths of significant groups. For example, posSignif[[2]] is a list containing the positions of the significant groups of size 2. Each list of this type further has two elements, fdr and bonf, corresponding to different multiple correction methods. Each element is a vector, of length the number of significant maximal cliques of a given size.

• MusGroup list of inferred mu values corresponding to the tested cliques, ordered ascending by the corresponding corrected p-value. The list contains as many elements as identified lengths of significant groups. For example, MusGroup[[2]] is a list containing the mu values of the significant maximal cliques of size 2. Each list of this type further has two elements, fdr and bonf, corresponding to different multiple testing correction methods. Each element is a vector, of length the number of significant maximal cliques of a given size.

• mcStruct input structure of maximal cliques to be tested for mutual exclusivity, as returned by doMaxCliques.

• matrix input binary alteration matrix.

• groupPvalue input threshold for the corrected p-value, lower than which cliques are significant.

Source

Produced with the function TiMEx, on the four binary matrices in the input dataset breastSubtypes.

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