sim_init: Simulation initialisation
In Moritz-Kohls/virDisco2: Virus Discovery

Description Usage Arguments Details Value Examples

Before the actual simulation procedure can start, statistical distributions of the original mapping results must be calculated by the function sim_init. The statistical distributions from the sam-files will be stored in the RDS objects directory, for each NGS run separately.

1	sim_init(file_indices = rep(NA_integer_, 0), type_of_sam_file)

`file_indices`	Indices of the sam-files to be analysed
`type_of_sam_file`	"init" for original sam-file or "sim" for sam-file of simulated fastq-files.

Before using the function sim_init, the functions create_directories_and_file_paths and extract_information_from_reference_genome must be executed.

None

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## Not run: sim_init(file_indices=1,type_of_sam_file="init") # Processing takes a few minutes of time!
## Not run: sim_init(file_indices=1,type_of_sam_file="sim") # Execute after mapping simulated fastq-files!

Moritz-Kohls/virDisco2 documentation built on Feb. 13, 2020, 12:32 a.m.