simSBS: Simulate single base substitutions
In simMP: Simulate Somatic Mutations in Cancer Genomes from Mutational Processes

Description Usage Arguments Value Examples

Given the number of genomes to be created, generate single base substitutions in those genomes from simulated mutational processes, by referring to a human reference genome.

simSBS(nSigs = NULL, nGenomes = NULL, refGenome = NULL,
        similarity = 0.6, noise = 0,
        presetSigs = NULL, chrs = NULL, nMutPerGenome = NULL,
        sigPrevalence = NULL, chrDistribution = NULL,
        parallel = TRUE, saveDir = './')

`nSigs`	Required. The number of mutational processes to be created.
`nGenomes`	Required. The number of genomes in which to simulate single base substitutions.
`refGenome`	Required. A `BSgenome` object of human reference genome.
`similarity`	Optional. Limit the similarity between any two mutational proccesses. 0 indicates no similarity while 1 indicates the opposite. Lower similarity may require more time to simulate.
`noise`	Optional. The value should between 0 and 1, indicating the amount of random mutations (noise) added to each simulated genome. 0 indicates no noise while 1 indicates the amount of noise is equal to the amount of mutation.
`presetSigs`	Optional. Use user defined mutational processes to simulate mutations in the genome. It should be a 96-by-n matrix, where 96 denotes the number of mutation motifs while n denotes the number of mutational processes. If presetSigs is given, nSigs = n.
`chrs`	Optional. On wich chromosome(s) mutations simulated from. Default is `c(1:22, 'X', 'Y')`. This argument accepts a vector that indicates chromosomes, which should be a vector created by manual input or, for example, using R code like `c(1:22, 'X', 'Y', 'M')`, where 'X', 'Y', 'M' are case sensitive (upper case) and indicate chromosome X, Y and mitochondrial chromosome. Incompatible input could cause fatal errors cause of unidentifiable chromosome name.
`nMutPerGenome`	Optional. NULL or a numerical vector whose length equals nGenomes. Number of mutations on each genome to simulate. If not defined, Default will use the distribution of number of single base substitutions in all WGS projects of ICGC release 23.
`sigPrevalence`	Optional. Acceptable values are either NULL or a numerical vector. The prevalence of mutational processes in wild. The default uses known prevalances of 21 processes from Alexandrov et al.'s work.
`chrDistribution`	Optional. NULL or a numerical vector are acceptable. The percentage of mutations assigned to each chromosome in a genome. The default uses the distribution of length of chromosomes (chr1 to chr22 and chrX and chrY). If a numerical vector was given, its length should equal the length of chrs and values should sum up to 1.
`parallel`	Optional. `TRUE` or `FALSE`. Whether enable or disable parallel computing ability.
`saveDir`	Optional. The directory where to save simulation output. Default is the current working directory. Other paths should also be relative to the current working directory.

If succeed, the return value is 1. Simulation results are saved in saveDir.

if(require(BSgenome.Hsapiens.UCSC.hg38)){
  simSBS(nSigs = 2, nGenomes = 2,
    refGenome = BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38,
    nMutPerGenome = sample(10:50, 2),
    parallel = FALSE)
}else{
  message('Cannot proceed withoud a valid reference genome.')
}