This function is used to check the arguments to be used for a run of sampletrees. If the options are properly specified, then sampletrees can be expected to run without errors from improper input files.
An object of class ‘pars’ with the arguments for the sampletrees run
Extensive checking is done, including:
- Non-default values have been provided for settings requiring user-specified values
- All input files exist
- All numeric settings are set to numeric values
- The format of the genotype and/or sequence files are correct
- The file with SNP locations contains only numeric values in increasing order, and that the number of locations matches the number of SNPs in the genotype/sequence file
- Focal point is set to a location in the region containing the SNPs
- Weights sum to 1 and the proposal indices are in the right range
Returns an object of class 'pars' with the 'clean' variable set to TRUE if the arguments in ‘args’ pass the error check and FALSE otherwise.
Burkett KM, McNeney B, Graham J. Sampletrees and Rsampletrees: sampling gene genealogies conditional on SNP genotype data. Bioinformatics. 32:1580-2, 2016
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# Will produce error messages runpars=newArgs() runpars=checkArgs(runpars) # Will not produce errors #system.file("Examples/sequences_Theta8_Rho8.txt",package="Rsampletrees") datname=paste(path.package("Rsampletrees"),"/extdata/sequences_Theta8_Rho8.txt",sep="") #system.file("Examples/locations_Theta8_Rho8.txt",package="Rsampletrees") locname=paste(path.package("Rsampletrees"),"/extdata/locations_Theta8_Rho8.txt",sep="") #system.file("Examples/weights-h.txt", package="Rsampletrees") weightname=paste(path.package("Rsampletrees"),"/extdata/weights-h.txt",sep="") runpars=newArgs(DataFile=datname, DataType="h", WeightFile=weightname, LocationFile=locname,RunName="Test-h",FocalPoint=10000) runpars=checkArgs(runpars)
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