shift: Shift the location of features in a GenBank record

In gschofl/biofiles: An Interface for GenBank/GenPept Flat Files

Description

Shift the location of features in a GenBank record

Usage

shift(x, shift = 0L, split = FALSE, order = TRUE, ...)

## S4 method for signature 'gbLocation'
shift(x, shift = 0L, split = FALSE, order = TRUE, ...)

## S4 method for signature 'gbFeature'
shift(x, shift = 0L, split = FALSE, order = TRUE, ...)

## S4 method for signature 'gbFeatureTable'
shift(x, shift = 0L, split = FALSE, order = FALSE)

## S4 method for signature '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.

Note

shift does not currently handle compound locations In a shifted feature table compound locations get merged.

Examples

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)

gschofl/biofiles documentation built on Sept. 27, 2020, 12:08 a.m.