biofiles (version 1.0.0)

shift: Shift the location of features in a GenBank record

Description

Shift the location of features in a GenBank record

Usage

shift(x, shift = 0L, split = FALSE, order = TRUE, ...)
# S4 method for gbLocation
shift(x, shift = 0L, split = FALSE, order = TRUE,
  ...)
# S4 method for gbFeature
shift(x, shift = 0L, split = FALSE, order = TRUE,
  ...)
# S4 method for gbFeatureTable
shift(x, shift = 0L, split = FALSE,
  order = FALSE)
# S4 method for gbRecord
shift(x, shift, split = FALSE, order = TRUE)

Arguments

x

A '>gbFeatureTable or '>gbRecord instance (gbFeatureTables must be complete and include a 'source' field).

shift

Number of basepairs (or aa residues) to shift.

split

Split features that after the shift extends across the end of the sequence.

order

Reorder features after the shift.

...

Additional arguments passed to methods.

Value

A '>gbFeatureTable object.

Examples

# NOT RUN {
load(system.file("extdata", "S_cerevisiae_mito.rda", package = "biofiles"))

## shift the S. cerevisiae mitochondrion such that cytochrome b is the first CDS
cytb <- start(filter(x, product = "^cytochrome b$")[[1]])[1]
x2 <- shift(x, shift = -cytb + 1, split = TRUE)
# }