coil (version 1.0.0)

indel_check: Check if coi5p sequence likely contains an indel error.

Description

Check if coi5p sequence likely contains an indel error.

Usage

indel_check(x, ...)
# S3 method for coi5p
indel_check(x, ..., indel_threshold = -358.88)

Arguments

x

a coi5p class object for which frame() and translate() have been run.

...

additional arguments to be passed between methods.

indel_threshold

the log likelihood threshold used to assess whether or not sequences are likely to contain an indel. Default is -358.88. Values lower than this will be classified as likely to contain an indel and values higher will be classified as not likely to contain an indel.

Value

an object of class "coi5p"

See Also

coi5p

frame

translate

Examples

# NOT RUN {
#previously run functions:
dat = coi5p(example_nt_string)
dat = frame(dat)
dat = translate(dat)
#current function
dat = indel_check(dat)
#with custom indel threshold
dat = indel_check(dat, indel_threshold = -400)
#additional components in output coi5p object:
dat$stop_codons #Boolean - Indicates if there are stop codons in the amino acid sequence.
dat$indel_likely #Boolean - Indicates if there is likely a insertion or deletion in the sequence.
dat$aaScore #view the amino acid log likelihood score
# }