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

In srnadiff: Finding differentially expressed unannotated genomic regions from RNA-seq data

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))

srnadiff documentation built on Jan. 7, 2021, 2 a.m.