checkArgs: Error checking for the arguments to sampletrees

In Rsampletrees: MCMC Sampling of Gene Genealogies Conditional on Genetic Data

Description

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.

Usage

checkArgs(args)

Arguments

args	An object of class ‘pars’ with the arguments for the sampletrees run

Details

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

Value

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.

Author(s)

Kelly Burkett

References

Burkett KM, McNeney B, Graham J. Sampletrees and Rsampletrees: sampling gene genealogies conditional on SNP genotype data. Bioinformatics. 32:1580-2, 2016

Examples

# 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)

Rsampletrees documentation built on March 3, 2020, 1:07 a.m.