parameters {srnadiff} | R Documentation

## Accessors for the 'parameters' slot of an srnadiffExp object

### Description

The `parameters` slot holds the parameter values used in an sRNA-diff approach as a named `list`. Default values exist for parameters, but these can also be supplied as input values in the `useParameters` argument of the `srnadiff` function or using the assignment function `parameters<-`.

### Usage

    ## S4 method for signature 'srnadiffExp'
    parameters(object)

    ## S4 replacement method for signature 'srnadiffExp'
    parameters(object) <- value

    ## S3 method for class 'srnadiff_par'
    print(x, ...)

### Arguments

`object` | An `srnadiffExp` object.
`value` | A named `list` containing valid parameters. See details.
`x` | The first element of the parameters used by an `srnadiff` object
`...` | The other elements of the parameters

### Details

Parameters in an sRNA-diff approach.

#### Global parameters

`minDepth`

  The cutoff to filter the base-level coverage. Bases where at least one sample has (normalized) coverage greater than `minDepth` be been retained. Default to `10`.

`minSize`

  The minimum size (in base-pairs) of the regions to be found. Default to `18`.

`maxSize`

  The maximum size (in base-pairs) of the regions to be found. Default to `1000000`.

`minGap`

  The minimum gap between regions. Regions separated by a gap of at most `minGap` positions are merged. Default to `100`.

`maxDiff`

  The maximum number of different bases between two regions. Near-identical regions are collapsed. Only regions with at most `maxDiff` different positions are considered identicals and are collapsed into one single region. Default to `20`.

`minOverlap`

  This parameters is used in the construction of the `countMatrix` matrix. Only reads (ranges) with a minimum of `minOverlap` overlapping each expressed region are considered to be overlapping. Default to `10`.

#### Parameters for the HMM method

`noDiffToDiff`

  Initial transition probability from no differentially expressed state to differentially expressed. Default to `0.001`.

`diffToNoDiff`

  Initial transition probability from differentially expressed state to no differentially expressed. Default to `0.000001`.

`emission`

  Emission probability. Default to `0.9`.

`emissionThreshold`

  Emission threshold. A real number between `0` and `1`. Default to `0.1`.

#### Parameters for the Naive and IR methods

`cutoff`

  The cutoff used in the naive method to determine candidate regions. Default to `1`.

`minLogFC`

  The minimun sliding threshold used in the IR method. Default to `0.5`.

### Value

The named list of the parameters used in the analysis.

### See Also

`useParameters` argument in `srnadiff` function.

### Examples

    srnaExp <- srnadiffExample()
    srnaExp <- srnadiff(srnaExp)
    print(parameters(srnaExp))

    parameters(srnaExp) <- list("minSize" = 1, "maxSize" = 1500)

    srnaExp <- srnadiffExample()
    srnaExp <- srnadiff(srnaExp)
    print(parameters(srnaExp))

[Package srnadiff version 1.11.0 Index]