This method simulates a wild-type sample sequencing in a phylogenetic forest.
Arguments
- phylo_forest
A phylogenetic forest.
- sequencer
The sequencer that performs the sequencing simulation (default: an
ErrorlessIlluminaSequencer).- chromosomes
The chromosomes that must be considered (default: all the reference chromosomes).
- coverage
The sequencing coverage (default:
10).- read_size
The read size (default:
150).- insert_size
The insert size. Use 0 for single read sequencing and any value greater than 0 for pair read sequencing (default:
0).- output_dir
The SAM output directory (default:
"rRACES_normal_SAM").- write_SAM
A Boolean flag to enable/disable SAM generation (default:
TRUE).- update_SAM
Update the output directory (default:
FALSE).- seed
The random seed for the internal random generator (optional).
Value
A dataframe representing, for each of the observed
SNVs, the chromosome and the position in which
it occurs (columns chr and chr_pos),
the SNV reference base, the alterate base, the causes,
and the classes of the SNV (columns ref_base, alt_base,
causes, and classes, respectively). Moreover, for each
of the sequencied samples <sample name>, the returned
dataframe contains three columns: the number of reads in
which the corresponding SNV occurs (column
<sample name>.occurrences), the coverage of the SNV
locus (column <sample name>.coverage), and the
corresponding VAF (column <sample name>.VAF).
See also
BasicIlluminaSequencer and
ErrorlessIlluminaSequencer as sequencer types, and
vignette("sequencing") for usage examples