compute_gene_localization: Computes localization of nonsynonymously mutated genes...

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

Description

Computes localization of nonsynonymously mutated genes passing thresholds of filter_genes

Usage

compute_gene_localization(
  TDAmut_object,
  num_permutations = 10000,
  num_cores = 1,
  seed = 121
)

Arguments

TDAmut_object	object of class TDAmut with expression data, mutation data, nerve complexes
num_permutations	number of permutations used to create null distribution when assessing localization of mutations in nerve complexes. By default is 10,000
num_cores	number of cores to be used in computation. By default is 1.
seed	integer specifying the seed used to initialize the generator of permutations. By default is 121

Value

Returns TDAmut object populated with Laplacian scores, p values, and q values for localization of genes passing thresholds of filter_genes. Outputs genes which are significantly localized.

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