BIGDAWG: Case-Control Analysis of Multi-Allelic Loci

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>.

Install the latest version of this package by entering the following in R:
install.packages("BIGDAWG")
AuthorDerek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>, Jill Hollenbach <Jill.Hollenbach@ucsf.edu>
Date of publication2016-08-31 01:18:29
MaintainerSteve Mack <sjmack@chori.org>
LicenseGPL (>= 3)
Version1.5.5
http://tools.immunogenomics.org/, https://github.com/pappasd/BIGDAWG

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...

Functions

A Man page
AA.df.check Man page
AAtable.builder Man page
AlignmentFilter Man page
AlignObj.Create Man page
AlignObj.Update Man page
A.wrapper Man page
BIGDAWG Man page
cci Man page
cci.pval Man page
cci.pval.list Man page
CheckAlleles Man page
CheckHLA Man page
CheckLoci Man page
CheckRelease Man page
DRB345.parser Man page
DRB345.zygosity Man page
Err.Log Man page
EVSremoval Man page
ExonPtnAlign.Create Man page
ExonPtnList Man page
getAllele.Count Man page
getCS.Mat Man page
getCS.stat Man page
GetField Man page
GetFiles Man page
getHap Man page
getObsFreq Man page
H Man page
HLA_data Man page
HWE Man page
HWE.ChiSq Man page
HWE.wrapper Man page
H.wrapper Man page
L Man page
L.wrapper Man page
make2x2 Man page
makeComb Man page
PgrpExtract Man page
PgrpFormat Man page
PreCheck Man page
rmABstrings Man page
RunChiSq Man page
TableMaker Man page
UpdateRelease Man page
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Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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