conserved_regions | R Documentation |
Returns the Conserved or the Non-conserved Regions from a MSA.
conserved_regions(x, ...)
## S4 method for signature 'Automorphism'
conserved_regions(
x,
conserved = TRUE,
output = c("all_pairs", "unique_pairs", "unique")
)
## S4 method for signature 'AutomorphismList'
conserved_regions(
x,
conserved = TRUE,
output = c("all_pairs", "unique_pairs", "unique"),
num.cores = multicoreWorkers(),
tasks = 0L,
verbose = FALSE
)
## S4 method for signature 'AutomorphismByCoef'
conserved_regions(
x,
conserved = TRUE,
output = c("all_pairs", "unique_pairs", "unique")
)
## S4 method for signature 'AutomorphismByCoefList'
conserved_regions(
x,
conserved = TRUE,
output = c("all_pairs", "unique_pairs", "unique")
)
x |
A |
... |
Not in use. |
conserved |
Logical, Whether to return the conserved or the non-conserved regions. |
output |
A character string. Type of output. |
num.cores , tasks |
Integers. Argument num.cores denotes the
number of cores to use, i.e. at most how many child processes will be run
simultaneously (see |
verbose |
logic(1). If TRUE, enable progress bar. |
A AutomorphismByCoef
class object containing the
requested regions.
## Load dataset
data("autm", package = "GenomAutomorphism")
conserved_regions(autm[1:3])
## Load automorphism found COVID datatset
data("covid_autm", package = "GenomAutomorphism")
## Conserved regions in the first 100 codons
conserv <- conserved_regions(covid_autm[1:100], output = "unique")
conserv
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