Set or get an Ensembl/BioMart handle on a qseaSet

Source: R/qseaExtra.R

Store and retrieve a “mart” handle inside a qseaSet for downstream annotation tasks (e.g., resolving gene coordinates).

setMart(object, ...)

# S4 method for class 'qseaSet'
setMart(object, mart)

getMart(object, ...)

# S4 method for class 'qseaSet'
getMart(object)

Arguments

object

qseaSet. The object to modify or query.

...

Additional arguments passed to methods or to biomaRt::useMart(). Not used in the default "qseaSet" method.

mart

biomaRt::Mart, character(1), or ANY. Connection object returned by biomaRt (recommended), or a string label you interpret elsewhere (e.g., "ENSEMBL_110"). Stored verbatim in object@parameters$mart. Default: none (must be supplied to setMart()).

Value

  • setMart() returns the updated qseaSet (with @parameters$mart set).

  • getMart() returns the stored value (whatever was set), or NULL if absent.

Details

These are S4 generics with methods for class "qseaSet". The value is not validated or dereferenced here; functions that consume it (e.g., gene annotation helpers) should perform any needed checks.

Methods

setMart(object, mart)

Set the handle on a qseaSet.

getMart(object)

Retrieve the stored handle from a qseaSet.

Examples

data(exampleTumourNormal, package = "mesa")

# Store a label (or use a real biomaRt::Mart) and read it back
exampleTumourNormal %>%
   setMart("ENSEMBL_110") %>%
   getMart()
#> [1] "ENSEMBL_110"