| fix_clonal_genotype {CIMICE} | R Documentation |
Fix the absence of the clonal genotype in the data (if needed)
fix_clonal_genotype(samples, freqs, labels)
samples |
input dataset (mutational matrix) as matrix |
freqs |
genotype frequencies (in the rows' order) |
labels |
list of gene names (in the columns' order) |
a named list containing the fixed "samples", "freqs" and "labels"
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)
# fix Colonal genotype absence, if needed
fix <- fix_clonal_genotype(samples, freqs, labels)
samples <- fix[["samples"]]
freqs <- fix[["freqs"]]
labels <- fix[["labels"]]
list("samples" = samples, "freqs" = freqs,
"labels" = labels, "genes" = genes)