utils-sequence {universalmotif} | R Documentation |
Sequence-related utility functions.
count_klets(string, k = 1, alph) get_klets(lets, k = 1) mask_seqs(seqs, pattern, RC = FALSE, letter = "-") shuffle_string(string, k = 1, method = c("euler", "linear", "markov"), rng.seed = sample.int(10000, 1))
string |
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k |
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alph |
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lets |
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seqs |
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pattern |
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RC |
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letter |
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method |
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rng.seed |
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For count_klets()
: A data.frame
with columns lets
and counts
.
For get_klets()
: A character
vector of k-lets.
For mask_seqs()
: The masked XStringSet
object.
For shuffle_string()
: A single character
string.
Benjamin Jean-Marie Tremblay, b2tremblay@uwaterloo.ca
create_sequences()
, shuffle_sequences()
####################################################################### ## count_klets ## Count k-lets for any string of characters count_klets("GCAAATGTACGCAGGGCCGA", k = 2) ## The default 'k' value (1) counts individual letters count_klets("GCAAATGTACGCAGGGCCGA") ####################################################################### ## get_klets ## Generate all possible k-lets for a set of characters get_klets(c("A", "C", "G", "T"), 3) ## Note that each element in 'lets' is considered a single unit; ## see: get_klets(c("AA", "B"), k = 2) ####################################################################### ## mask_seqs ## Mask repetitive seqeuences data(ArabidopsisPromoters) mask_seqs(ArabidopsisPromoters, "AAAAAA") ####################################################################### ## shuffle_string ## Shuffle any string of characters shuffle_string("ASDADASDASDASD", k = 2)