Description Usage Arguments Value
Simulate DNA sequences with an enriched motif
1 2 3 | 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)
|
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) |
a character vector of random DNA sequences with an enriched motif
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