create_tbl_ent_clones: Get clone alteration tibble.

In GeneAccord: Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients

Description

Creates a tibble containing the information of which genes/pathways are altered in a patient in which clone.

Usage

create_tbl_ent_clones(path_to_file, max_num_clones = 7)

Arguments

path_to_file	The path to the file with the table of altered genes/pathways and their clone affiliation.
max_num_clones	The upper bound for the number of clones that were found per tumor. Default: 7.

Details

It expects a comma-separated table where the first column is the name of the altered gene or pathway. The other columns are for the clones in the respective tumor. Such a table can be generated with a tool that identifies clones in tumor samples, e.g. Cloe.

The table is expected to be comma-separated and to have the columns 'altered_entity', 'clone1', 'clone2', ..., 'cloneN', depending on how many clones were detected in the respective tumor. Each row then contains in the first column the name of the mutated gene or affected pathway, e.g. "ENSG00000134086", and in the other columns it has either zeros or ones, indicating in which clone the respective gene/pathway is altered.

Value

The tibble containing the information of which gene/pathway is altered in which clone in a patient. Has the columns 'file_name', 'patient_id', 'altered_entity', 'clone1', 'clone2', ... up to the maximal number of clones (Default: until 'clone7'). Note that the labelling of the clones does not matter and only needs to stay fixed within each patient and tree inference.

Author(s)

Ariane L. Moore

Examples

ext_data_dir <- system.file('extdata', package='GeneAccord')
create_tbl_ent_clones(paste(ext_data_dir, 
    "/clonal_genotypes/cloe_seed5/01.csv", sep=""))

GeneAccord documentation built on Nov. 8, 2020, 8:04 p.m.