TDAmut-class: Class to handle all information in the TDAmut pipeline

In CamaraLab/TDA-TCGA: An R package for identification of relevant genetic alterations in cancer using topological data analysis

Description

Class to handle all information in the TDAmut pipeline

Slots

expression_table

Expression data data.frame or matrix (create_TDAmut_object)

mutation_table

Mutation data table (create_TDAmut_object)

nerve_complexes

Topological representations as nerve complexes (compute_complexes)

mapper_intervals

Range of intervals used in TDAmapper (compute_complexes)

mapper_percents

Range of percent overlaps used in TDAmapper (compute_complexes)

filter_embedding

Embedding used to create topological representations in TDAmapper (compute_complexes)

mutation_matrix

Reformatted mutation data (create_TDAmut_object)

nonsyn_mutations

Reformatted nonsynonymous mutation data (create_TDAmut_object)

syn_mutations

Reformatted synonymous mutation data (create_TDAmut_object)

mutational_load

Total mutations per sample (create_TDAmut_object)

mutational_load_localization

p and q values indicating significance of mutational load localization across the parameter space (compute_complexes)

correlations

p and q values indicating significance of negative correlation between expression and mutation data of a given gene across the parameter space (filter_genes)

filtered_genes

Genes passing user-defined thresholds on mutational frequency, ratio of nonsynonymous / total mutations, and correlation q values (filter_genes)

gene_scores

p and q values indicating significance of localization of nonsynonymously mutated genes across the parameter space (compute_gene_localization)

summary_matrix

Matrix summarizing the results of the pipelinesin the computation (compute_gene_localization)

CamaraLab/TDA-TCGA documentation built on Oct. 30, 2021, 5:14 p.m.