BIGDAWG {BIGDAWG}

BIGDAWG Main Wrapper Function

Description

This is the main wrapper function for each analysis.

Usage

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
)

Arguments

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.

Examples

## 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)