fix_clonal_genotype {CIMICE} | R Documentation

## Manage Clonal genotype in data

### Description

Fix the absence of the clonal genotype in the data (if needed)

### Usage

    fix_clonal_genotype(samples, freqs, labels, matching_samples)

### Arguments

`samples` | input dataset (mutational matrix) as matrix
`freqs` | genotype frequencies (in the rows' order)
`labels` | list of gene names (in the columns' order)
`matching_samples` | list of sample names matching each genotype

### Value

a named list containing the fixed "samples", "freqs" and "labels"

### 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)
    if( is.null(compactedDataset$row_names) ){
      compactedDataset$row_names <- rownames(compactedDataset$matrix)
    }
    matching_samples <- compactedDataset$row_names
    # matching_samples
    matching_samples

    # fix Colonal genotype absence, if needed
    fix <- fix_clonal_genotype(samples, freqs, labels, matching_samples)

[Package CIMICE version 1.2.1 Index]