BIGDAWG: Case-Control Analysis of Multi-Allelic Loci

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Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids) as described in Pappas DJ, Marin W, Hollenbach JA, Mack SJ (2016) <doi:10.1016/j.humimm.2015.12.006>. Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA (2012) <doi:10.1007/978-1-61779-842-9_14>.

Author
Derek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>, Jill Hollenbach <Jill.Hollenbach@ucsf.edu>
Date of publication
2016-08-31 01:18:29
Maintainer
Steve Mack <sjmack@chori.org>
License
GPL (>= 3)
Version
1.5.5
URLs

View on CRAN

Man pages

A
Amino Acid Analysis Function
AA.df.check
Contingency Table Check
AAtable.builder
Amino Acid Contingency Table Build
AlignmentFilter
Alignment Filter
AlignObj.Create
Alignment Object Creator
AlignObj.Update
Updated Alignment Object Creator
A.wrapper
Amino Acid Wrapper
BIGDAWG
BIGDAWG wrapper function
cci
Case-Control Odds ratio calculation and graphing
cci.pval
Case Control Odds Ratio Calculation from Epicalc
cci.pval.list
Case Control Odds Ratio Calculation from Epicalc list...
CheckAlleles
Allele presence check
CheckHLA
HLA formatting check
CheckLoci
Loci presence check
CheckRelease
Function to Check Release Versions
DRB345.parser
DRB345 Column Processing
DRB345.zygosity
DRB345 haplotype zygosity checker
Err.Log
Error Code Display and Logging
EVSremoval
Expression Variant Suffix Removal
ExonPtnAlign.Create
Protein Exon Alignment Formatter
ExonPtnList
Exon 2 (class II) or 2/3 (class I) protein alignments.
getAllele.Count
Recompute number of alleles
getCS.Mat
Chi square matrices
getCS.stat
Chi square test statistic
GetField
HLA trimming function
GetFiles
File Fetcher
getHap
Haplotype Table Maker
getObsFreq
Observed Frequency
H
Haplotype Analysis Function
HLA_data
Example HLA Dataset
HWE
Hardy Weinbergy Equilibrium Function
HWE.ChiSq
Hardy Weinbergy Equilibrium Function
HWE.wrapper
Hardy-Weinbery Wrapper
H.wrapper
Haplotype Wrapper
L
Locus Analysis Function
L.wrapper
Locus Wrapper
make2x2
Creation of a 2x2 table using the indicated orientation.
makeComb
Genotype Combination Maker
PgrpExtract
HLA P group Finder
PgrpFormat
HLA P group File Formatter
PreCheck
Data summary function
rmABstrings
Replace absent allele strings
RunChiSq
Chi-squared Contingency Table Test
TableMaker
Table Maker
UpdateRelease
Update function for protein aligment upon new IMGT HLA data...

Files in this package

BIGDAWG
BIGDAWG/inst
BIGDAWG/inst/doc
BIGDAWG/inst/doc/BIGDAWG.Rmd
BIGDAWG/inst/doc/BIGDAWG.html
BIGDAWG/NAMESPACE
BIGDAWG/NEWS
BIGDAWG/R
BIGDAWG/R/BIGDAWG.R
BIGDAWG/R/A_wrapper.R
BIGDAWG/R/general_functions.R
BIGDAWG/R/CheckRelease.R
BIGDAWG/R/L.R
BIGDAWG/R/sysdata.rda
BIGDAWG/R/L_wrapper.R
BIGDAWG/R/data.R
BIGDAWG/R/A_ExonPtnAlign_functions.R
BIGDAWG/R/H.R
BIGDAWG/R/A_support_functions.R
BIGDAWG/R/A.R
BIGDAWG/R/HWE_wrapper.R
BIGDAWG/R/update_wrapper.R
BIGDAWG/R/epicalc.R
BIGDAWG/R/check_functions.R
BIGDAWG/R/H_support_functions.R
BIGDAWG/R/HWE_support_functions.R
BIGDAWG/R/H_wrapper.R
BIGDAWG/R/HWE.R
BIGDAWG/vignettes
BIGDAWG/vignettes/BIGDAWG.Rmd
BIGDAWG/MD5
BIGDAWG/build
BIGDAWG/build/vignette.rds
BIGDAWG/DESCRIPTION
BIGDAWG/man
BIGDAWG/man/HWE.wrapper.Rd
BIGDAWG/man/L.wrapper.Rd
BIGDAWG/man/cci.Rd
BIGDAWG/man/getAllele.Count.Rd
BIGDAWG/man/PgrpFormat.Rd
BIGDAWG/man/HWE.ChiSq.Rd
BIGDAWG/man/AlignObj.Update.Rd
BIGDAWG/man/RunChiSq.Rd
BIGDAWG/man/HLA_data.Rd
BIGDAWG/man/cci.pval.list.Rd
BIGDAWG/man/GetField.Rd
BIGDAWG/man/ExonPtnList.Rd
BIGDAWG/man/H.wrapper.Rd
BIGDAWG/man/HWE.Rd
BIGDAWG/man/ExonPtnAlign.Create.Rd
BIGDAWG/man/BIGDAWG.Rd
BIGDAWG/man/UpdateRelease.Rd
BIGDAWG/man/CheckHLA.Rd
BIGDAWG/man/DRB345.parser.Rd
BIGDAWG/man/CheckAlleles.Rd
BIGDAWG/man/EVSremoval.Rd
BIGDAWG/man/DRB345.zygosity.Rd
BIGDAWG/man/getObsFreq.Rd
BIGDAWG/man/CheckLoci.Rd
BIGDAWG/man/PreCheck.Rd
BIGDAWG/man/AlignmentFilter.Rd
BIGDAWG/man/getHap.Rd
BIGDAWG/man/H.Rd
BIGDAWG/man/CheckRelease.Rd
BIGDAWG/man/PgrpExtract.Rd
BIGDAWG/man/AAtable.builder.Rd
BIGDAWG/man/TableMaker.Rd
BIGDAWG/man/L.Rd
BIGDAWG/man/A.wrapper.Rd
BIGDAWG/man/GetFiles.Rd
BIGDAWG/man/rmABstrings.Rd
BIGDAWG/man/getCS.stat.Rd
BIGDAWG/man/getCS.Mat.Rd
BIGDAWG/man/AA.df.check.Rd
BIGDAWG/man/makeComb.Rd
BIGDAWG/man/cci.pval.Rd
BIGDAWG/man/AlignObj.Create.Rd
BIGDAWG/man/make2x2.Rd
BIGDAWG/man/Err.Log.Rd
BIGDAWG/man/A.Rd