Package: BIGDAWG 3.0.8

Steve Mack

BIGDAWG: Case-Cotrol 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>.

Authors:Derek Pappas <[email protected]>, Steve Mack <[email protected]>, Jill Hollenbach <[email protected]>

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BIGDAWG/json (API)
NEWS

Peer review:

Bug tracker:https://github.com/igdawg/bigdawg/issues

On CRAN:

77 exports 2 stars 2.44 score 85 dependencies 2 dependents 7 mentions 4 scripts 455 downloads

Last updated 1 years agofrom:518e3b3805. Checks:OK: 1 WARNING: 6. Indexed: yes.

Exports:AA.wrapperAA.df.checkAA.df.csAAtable.builderAlignmentFilterAlignObj.CreateAlignObj.UpdateAppend.SystemBIGDAWGBuild.MatrixbuildHAPnamesbuildHAPsetsccicci.pvalcci.pval.listCheck.CoresCheck.DataCheck.ParamsCheck.Params.GLSCheckAllelesCheckHLACheckLociCheckReleaseCheckString.AlleleCheckString.LocusCondense.EPLCreate.Null.TableDRB345.Check.WrapperDRB345.Check.ZygosityDRB345.ExpDRB345.parserErr.LogEVSremovalExon.FilterExonPtnAlign.CreateExonPtnListFillerFormat.AlleleFormat.TabgetAllele.CountgetCS.MatgetCS.statGetFieldgetFileNameGetFilesgetHapgetObsFreqGL2Tab.LociGL2Tab.SubGL2Tab.wrapperGLSconvertH.MCH.MC.wrapperHLA_dataHWEHWE.ChiSqHWE.wrapperLL.wrappermake2x2makeCombMergeData_OutputPgrpExtractPgrpFormatPreCheckprepDatarmABstringsRunChiSqRunChiSq_cStrippersummaryGeno.2Tab2GL.LociTab2GL.SubTab2GL.wrapperTableMakerUpdateRelease

Dependencies:arsenalaskpassbackportsbase64encbslibcachemcheckmatecliclustercodetoolscolorspacecurldata.tabledigestevaluatefansifarverfastmapfontawesomeforeignFormulafsggplot2gluegridExtragtablehaplo.statshighrHmischtmlTablehtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixMatrixModelsmemoisemgcvmimemultcompmunsellmvtnormnlmennetopensslpillarpkgconfigpolsplinequantregR6rappdirsRColorBrewerrlangrmarkdownrmsrpartrstudioapisandwichsassscalesSparseMstringistringrsurvivalsysTH.datatibbletinytexutf8vctrsviridisviridisLitewithrxfunXMLyamlzoo