Getting the sampled cells mutations

This method returns the mutations of the sample cells.

Arguments

cell_id

The identifier of the cell whose mutations are aimed (optional).

Value

A dataframe reporting cell_id, chr, (i.e., the mutation chromosome), chr_pos (i.e., position in the chromosome), allele

(in which the mutation occurs), ref, alt, type (i.e., either "SNV" or "indel"), cause, and class (i.e., "driver", "passenger", "germinal" or "preneoplastic") for each mutation in the sampled cell genomes.

Details

This method builds a dataframe representing all the SNV and the indel mutations in the cells sampled during the simulation and represented by the leaves of the phylogenetic forest. The dataframe also reports the allele in which the mutations occur to support double occurrencies due to CNAs.

See also

vignette("mutations") for usage examples