shmulateSeq {shazam}

Simulate mutations in a single sequence

Description

Generates random mutations in a sequence iteratively using a targeting model. Targeting probabilities at each position are updated after each iteration.

Usage

shmulateSeq(
  sequence,
  numMutations,
  targetingModel = HH_S5F,
  start = 1,
  end = nchar(sequence),
  frequency = FALSE
)

Arguments

sequence

sequence string in which mutations are to be introduced. Accepted alphabet: {A, T, G, C, N, .}. Note that - is not accepted.

numMutations

a whole number indicating the number of mutations to be introduced into sequence, if frequency=FALSE. A fraction bewteen 0 and 1 indicating the mutation frequency if frequency=TRUE.

targetingModel

5-mer TargetingModel object to be used for computing probabilities of mutations at each position. Defaults to HH_S5F.

start

Initial position in sequence where mutations can be introduced. Default: 1

end

Last position in sequence where mutations can be introduced. Default: last position (sequence length).

frequency

If TRUE, treat numMutations as a frequency.

Details

If the input sequence has a non-triplet overhang at the end, it will be trimmed to the last codon. For example, ATGCATGC will be trimmed to ATGCAT.

Mutations are not introduced to positions in the input sequence that contain . or N.

With frequency=TRUE, the number of mutations introduced is the floor of the length of the sequence multiplied by the mutation frequency specified via numMutations.

Value

A string defining the mutated sequence.

See Also

See shmulateTree for imposing mutations on a lineage tree. See HH_S5F and MK_RS5NF for predefined TargetingModel objects.

Examples

# Define example input sequence
sequence <- "NGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGATA.TTTA"

# Simulate using the default human 5-mer targeting model
# Introduce 6 mutations
shmulateSeq(sequence, numMutations=6, frequency=FALSE)

# Introduction 5% mutations
shmulateSeq(sequence, numMutations=0.05, frequency=TRUE)