BIGDAWG (version 1.2.6)

BIGDAWG: BIGDAWG wrapper function

Description

This is the main wrapper function for each analysis.

Usage

BIGDAWG(Data, HLA = TRUE, Run.Tests, Loci.Set, All.Pairwise = FALSE,
  Trim = FALSE, Res = 2, EVS.rm = FALSE, Missing = 0, Cores.Lim = 1L,
  Results.Dir, Output = 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).

All.Pairwise

Logical indicating whether all pairwise.

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").

Cores.Lim

Interger setting the number of cores accessible to BIGDAWG (Windows, Cores = 1L).

Results.Dir

Optional, full directory name for BIGDAWG output.

Output

Logical indicating if data should be written to output directory (mainly used for testing).

Examples

### The following examples use the synthetic data set bundled with BIGDAWG

# Haplotype analysis with no missing genotypes for two loci
# Significant haplotypic 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 associations with phenotype at all but DQB1
BIGDAWG(Data="HLA_data", Run.Tests=c("HWE","L"), Missing="ignore")

# Hardy-Weinberg analysis trimming data to 2-Field resolution
# Significant deviation at DQB1
BIGDAWG(Data="HLA_data", Run.Tests="HWE", Trim=TRUE, Res=2)