getFeatureSetCommands {iSEEu} | R Documentation

## Global feature set commands

### Description

Get or set the commands to define the global collection of feature sets.

### Usage

    getFeatureSetCommands()

    setFeatureSetCommands(value)

### Arguments

`value` | A list of two character vectors named `"CreateCollections"` and `"RetrieveSet"`. Both vectors should be of the same length and have the same names. Vectors should contain R commands to create collections and retrieve sets; see `?FeatureSetTable` and the output of `createGeneSetCommands` for details.

### Details

These utilities allow users to easily set the feature set commands for all FeatureSetTables at once. Any global settings only take effect (i) during setup of the `iSEE` application and (ii) if the first FeatureSetTable does not have an existing values in the `"CreateCollections"` or `"RetrieveSet"` slots.

### Value

`getFeatureSetCommands` returns the current global feature set commands.

`setFeatureSetCommands` will set the current global feature set commands and return `NULL` invisibly.

### Author(s)

Aaron Lun

### See Also

`createGeneSetCommands`, for one method of generating `value`.

### Examples

    old <- getFeatureSetCommands()

    new.cmds <- createGeneSetCommands(organism="org.Mm.eg.db",
        identifier="SYMBOL")
    setFeatureSetCommands(new.cmds)

    getFeatureSetCommands()

    setFeatureSetCommands(old)

[Package iSEEu version 1.2.0 Index]