Description Usage Arguments Examples
This is the main wrapper function for each analysis.
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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. |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## 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)
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