BIGDAWG: BIGDAWG Main Wrapper Function
In BIGDAWG: Case-Control Analysis of Multi-Allelic Loci

This is the main wrapper function for each analysis.

BIGDAWG(
  Data,
  HLA = TRUE,
  Run.Tests,
  Loci.Set,
  Exon,
  All.Pairwise = FALSE,
  Trim = FALSE,
  Res = 2,
  EVS.rm = FALSE,
  Missing = 2,
  Strict.Bin = FALSE,
  Cores.Lim = 1L,
  Results.Dir,
  Return = FALSE,
  Output = TRUE,
  Merge.Output = FALSE,
  Verbose = TRUE
)

`Data`	Name of the genotype data file.
`HLA`	Logical Indicating whether data is HLA class I/II genotyping data only.
`Run.Tests`	Specifics which tests to run.
`Loci.Set`	Input list defining which loci to use for analyses (combinations permitted).
`Exon`	Numeric Exon(s) for targeted amino acid analysis.
`All.Pairwise`	Logical indicating whether all pairwise loci should be analyzed in haplotype analysis.
`Trim`	Logical indicating if HLA alleles should be trimmed to a set resolution.
`Res`	Numeric setting what desired resolution to trim HLA alleles.
`EVS.rm`	Logical indicating if expression variant suffixes should be removed.
`Missing`	Numeric setting allowable missing data for running analysis (may use "ignore").
`Strict.Bin`	Logical specify if strict rare cell binning should be used in ChiSq test.
`Cores.Lim`	Integer setting the number of cores accessible to BIGDAWG (Windows limit is 1 core).
`Results.Dir`	Optional, string of full path directory name for BIGDAWG output.
`Return`	Logical Should analysis results be returned as list.
`Output`	Logical Should analysis results be written to output directory.
`Merge.Output`	Logical Should analysis results be merged into a single file for easy access.
`Verbose`	Logical Should a summary of each analysis be displayed in console.

## Not run: 
### The following examples use the synthetic data set bundled with BIGDAWG

# Haplotype analysis with no missing genotypes for two loci sets
# Significant haplotype association with phenotype
# BIGDAWG(Data="HLA_data", Run.Tests="H", Missing=0, Loci.Set=list(c("DRB1","DQB1")))

# Hardy-Weinberg and Locus analysis ignoring missing data
# Significant locus associations with phenotype at all but DQB1
# BIGDAWG(Data="HLA_data", Run.Tests="L", Missing="ignore")

# Hardy-Weinberg analysis trimming data to 2-Field resolution with no output to files (console only)
# Significant locus deviation at DQB1
BIGDAWG(Data="HLA_data", Run.Tests="HWE", Trim=TRUE, Res=2, Output=FALSE)

## End(Not run)