Convert a BEIDList object in a specific identifier (BEID) scope

Usage

# S3 method for class 'BEIDList'
focusOnScope(
  x,
  be = NULL,
  source = NULL,
  organism = NULL,
  scope = NULL,
  force = FALSE,
  restricted = TRUE,
  prefFilter = TRUE,
  ...
)

Arguments

x

the BEIDList to be converted

be

the type of biological entity to focus on. If NULL (default), it's taken from scope(x). Used if is.null(scope)

source

the source of BEID to focus on. If NULL (default), it's taken from scope(x). Used if is.null(scope)

organism

the organism of BEID to focus on. If NULL (default), it's taken from scope(x). Used if is.null(scope)

scope

a list with the following element:

be
source
organism

force

if TRUE the conversion is done even between identical scopes (default: FALSE)

restricted

if TRUE (default) the BEID are limited to current version of the source

prefFilter

if TRUE (default) the BEID are limited to prefered identifiers when they exist

...

additional parameters to the BEID conversion function

Value

A BEIDList