createFakeDNA: Create fake DNA or amino acid sequences

In sherrillmix/dnaplotr: Plot a Collection of DNA Sequences

Create fake DNA or amino acid sequences

Description

Creates a random reference sequence then adds mutations and indels to hierarchical sets of the sequences and random noise

Usage

createFakeDNA(
  n = 500,
  nChar = 400,
  nSplit = 3,
  pGap = 0.3,
  pNoise = 0.01,
  pMutation = 0.005,
  bases = c("A", "C", "T", "G", "-"),
  excludeBases = c("-", "X")
)

createFakeAA(
  n = 100,
  nChar = 100,
  ...,
  pGap = 0.2,
  pNoise = 0,
  pMutation = 0.01,
  bases = c(names(dnaplotr::aminoCols), "-")
)

Arguments

n	number of fake sequences to generate
nChar	character length of the output fake sequences
nSplit	The number of hierarchical splits to make in the data e.g. 3 splits produces 2^3=8 "species"
pGap	probability of a large insertion or deletion in each grouping
pNoise	probability of a random substitution at each base
pMutation	probability of a substitution at each base in each hierarchical grouping
bases	the bases used in generating the sequence (bases listed in excludeBases are excluded from the initial reference sequence generation
excludeBases	bases excluded from the initial reference sequence generation (default: '-' and 'X')
...	additional arguments to createFakeDNA

Value

A n+1 length character vector of fake sequences. The first sequence is the reference. Names of the remaining sequences indicate their hierarchical groupings follow by an arbitrary id

Examples

createFakeDNA(10,10)
createFakeAA(10,10)

sherrillmix/dnaplotr documentation built on Oct. 29, 2022, 4:42 p.m.