settings {RNAmodR} | R Documentation

## Settings for `Modifier` objects

### Description

Depending on data prepation, quality and desired stringency of a modification strategy, settings for cut off parameters or other variables may need to be adjusted. This should be rarely the case, but a function for changing these settings, is implemented as the... `settings` function.

For changing values the input can be either a `list` or something coercible to a `list`. Upon changing a setting, the validity of the value in terms of type(!) and dimensions will be checked.

If settings have been modified after the data was loaded, the data is potentially invalid. To update the data, run the `aggregate` or the `modify` function.

### Usage

    settings(x, name = NULL)

    settings(x, name) <- value

    ## S4 method for signature 'Modifier'
    settings(x, name = NULL)

    ## S4 replacement method for signature 'Modifier'
    settings(x) <- value

    ## S4 method for signature 'ModifierSet'
    settings(x, name = NULL)

    ## S4 replacement method for signature 'ModifierSet'
    settings(x) <- value

### Arguments

`x` | a `Modifier` or `ModifierSet` class
`name` | name of the setting to be returned or set
`value` | value of the setting to be set

### Value

If `name` is omitted, `settings` returns a list of all settings. If `name` is set, `settings` returns a single settings or `NULL`, if a value for `name` is not available.

### Examples

    data(msi,package="RNAmodR")
    mi <- msi[[1]]
    # returns a list of all settings
    settings(mi)
    # accesses a specific setting
    settings(mi,"minCoverage")
    # modification of setting
    settings(mi) <- list(minCoverage = 11L)

[Package RNAmodR version 1.2.3 Index]