simulate_sequences: Simulate DNA sequences with an enriched motif

Description Usage Arguments Value

Description

Simulate DNA sequences with an enriched motif

Usage

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simulate_sequences(motif, number_sequences = 300,
  sequence_length = 200, motif_position = NULL, enrichment = 0.5,
  jitter = 10, highprob = 0.85, lowprob = 0.6, randomstrand = TRUE)

Arguments

motif

character; string containing the motif sequence, can be upper or lower case ACGT or _

number_sequences

numeric; number of sequences to generate

sequence_length

numeric; length in bases of the sequences to be generated

motif_position

numeric; start position of the motif in the sequences, default is half the sequence length - half the motif width

enrichment

numeric; what fraction of sequences should include the motif

jitter

integer; how many base pairs to randomly +/- shift the position of the motif

highprob

numeric; probability (between 0 and 1) of choosing a base when the motif has a capital/uppercase letter

lowprob

numeric; probability (between 0 and 1) of choosing a base when the motif has a lowercase letter

randomstrand

logical; should the strand of the motif be randomised (default: TRUE)

Value

a character vector of random DNA sequences with an enriched motif


MyersGroup/MotifFinder documentation built on June 7, 2019, 3:42 p.m.