prepare_labels: Prepare node labels based on genotypes

In redsnic/CIMICE: CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution

Prepare node labels based on genotypes

Description

Prepare node labels so that each node is labelled with a comma separated list of the alterated genes representing its associated genotype.

Usage

prepare_labels(samples, genes)

Arguments

samples	input dataset (mutational matrix) as matrix
genes	list of gene names (in the columns' order)

Details

Note that after this procedure the user is expected also to run fix_clonal_genotype to also add the clonal genortype to the mutational matrix if it is not present.

Value

the computed edge list

Examples

require(dplyr) 

# compact
compactedDataset <- compact_dataset(example_dataset())
samples <- compactedDataset$matrix

# save genes' names
genes <- colnames(compactedDataset$matrix)

# keep the information on frequencies for further analysis
freqs <- compactedDataset$counts/sum(compactedDataset$counts)

# prepare node labels listing the mutated genes for each node
labels <- prepare_labels(samples, genes)

redsnic/CIMICE documentation built on March 30, 2022, 2:46 a.m.