getDefaultParameterList: Helper function to generate a default parameter list as input...

In SNPhood: SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data

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"

SNPhood documentation built on Nov. 8, 2020, 6:22 p.m.