getDefaultParameterList {SNPhood} | R Documentation

## Helper function to generate a default parameter list as input for the function analyzeSNPhood

### Description

`getDefaultParameterList` generates a default parameter list that can be used as input for the function `analyzeSNPhood`. The path to the user regions file can optionally be provided as an argument to the function. See the examples for further details. Before running the function `analyzeSNPhood`, carefully check that the default parameters are suitable for the analysis.

### Usage

    getDefaultParameterList(path_userRegions = NULL, isPairedEndData = TRUE)

### Arguments

`path_userRegions` | Character(1). Specify the value of the parameter `path_userRegions` (absolute path to the user regions file, see the Vignette for details).
`isPairedEndData` | Logical(1). Default TRUE. Are the data paired-end (TRUE) or single-end (FALSE)?

### Value

a named list with default values for the currently supported parameters that can be used as input for the function `analyzeSNPhood`:

- readFlag_isPaired: Logical(1), TRUE for paired-end data, NA for single-end

- readFlag_isProperPair: Logical(1), TRUE

- readFlag_isUnmappedQuery: Logical(1), FALSE

- readFlag_hasUnmappedMate: Logical(1), FALSE

- readFlag_isMinusStrand: Logical(1), NA

- readFlag_isMateMinusStrand: Logical(1), NA

- readFlag_isFirstMateRead: Logical(1), NA

- readFlag_isSecondMateRead: Logical(1), NA

- readFlag_isNotPrimaryRead: Logical(1), FALSE

- readFlag_isNotPassingQualityControls: Logical(1), FALSE

- readFlag_isDuplicate: Logical(1), FALSE

- readFlag_reverseComplement: Logical(1), FALSE

- readFlag_simpleCigar: Logical(1), TRUE

- path_userRegions: Character(1), as given by the function argument path_userRegions

- zeroBasedCoordinates: Logical(1), FALSE

- regionSize: Integer(1), 500

- binSize: Integer(1), 50

- readGroupSpecific: Logical(1), TRUE

- strand: Character(1), "both"

- startOpen: Logical(1), FALSE

- endOpen: Logical(1), FALSE

- headerLine: Logical(1), FALSE

- linesToParse: Integer(1), -1

- lastBinTreatment: Character(1), "delete"

- assemblyVersion: Character(1), "hg19"

- nCores: Integer(1), 1

- keepAllReadCounts: Logical(1), FALSE

- normByInput: Logical(1), FALSE

- normAmongEachOther: Logical(1), TRUE

- poolDatasets: Logical(1), FALSE

For reasons of reduced redundancy, a detailed description of the parameters can be found at the end of the main vignette in `SNPhood` (`browseVignettes("SNPhood")`).

### See Also

`analyzeSNPhood`

### Examples

    ## Only one parameter can, optionally, be specified when calling the function
    par.l = getDefaultParameterList(path_userRegions = "path/to/regions", isPairedEndData = TRUE)
    ## If the file is not specified, you need to change it
    ## before you can execute the function \code{\link{analyzeSNPhood}}
    par.l = getDefaultParameterList(isPairedEndData = TRUE)
    par.l$path_userRegions = "path/to/regions"

[Package SNPhood version 1.16.0 Index]