Entry: GGfitter-class
Aliases: GGfitter-class fastAGM fastHET fastAGMfitter fastHETfitter snpScreen,racExSet,snpMeta,genesym,formula,GGfitter,ANY-method
Keywords: classes
Description: Class "GGfitter" wrapper for special functions to do whole genome screens
URL: ../../../library/GGtools/html/GGfitter-class.html

Entry: HM2rac
Aliases: HM2rac thinHM2rac thinHM2meta df2snpMeta getRare countRare
Keywords: models
Description: compute rare allele count from a hapmap file
URL: ../../../library/GGtools/html/HM2rac.html

Entry: HMworkflow
Aliases: HMworkflow
Keywords: models
Description: function to bind together HapMap genotyping results and expression data
URL: ../../../library/GGtools/html/HMworkflow.html

Entry: Strains2rac
Aliases: Strains2rac INBREDSworkflow INB34snpMeta
Keywords: models
Description: convert a Wellcome 'Strains' genotyping file to rare allele count form
URL: ../../../library/GGtools/html/Strains2rac.html

Entry: geneLocs
Aliases: geneLocs geneLocs_hsa geneLocs_mmu
Keywords: models
Description: gene metadata from NCBI
URL: ../../../library/GGtools/html/geneLocs.html

Entry: genoStrings
Aliases: genoStrings
Keywords: models
Description: create a character vector of genotype value strings
URL: ../../../library/GGtools/html/genoStrings.html

Entry: gwSnpScreen-methods
Aliases: gwSnpScreen-methods gwSnpScreen cwSnpScreen cnumOrMissing-class gwSnpScreen,genesym,smlSet-method gwSnpScreen,genesym,smlSet,cnumOrMissing-method gwSnpScreen,GeneSet,smlSet,cnumOrMissing-method
Keywords: methods models
Description: genome-wide test for association between SNP and phenotype
URL: ../../../library/GGtools/html/gwSnpScreen-methods.html

Entry: gwSnpScreenResult-class
Aliases: gwSnpScreenResult-class multiGwSnpScreenResult-class cwSnpScreenResult-class plot,gwSnpScreenResult,ANY-method plot,cwSnpScreenResult,ANY-method plot,gwSnpScreenResult-method plot,cwSnpScreenResult-method show,gwSnpScreenResult-method getAbsSnpLocs,cwSnpScreenResult-method getAbsSnpLocs show,multiGwSnpScreenResult-method [,gwSnpScreenResult-method [,gwSnpScreenResult,ANY,ANY-method
Keywords: classes
Description: Class "gwSnpScreenResult" -- containers for genome-wide and chromosome-wide snp screen statistics
URL: ../../../library/GGtools/html/gwSnpScreenResult-class.html

Entry: make_racExSet
Aliases: make_racExSet rb20M Sa20M
Keywords: models
Description: create a racExSet from simpler constituents
URL: ../../../library/GGtools/html/make_racExSet.html

Entry: oGtypeExSet-class
Aliases: oGtypeExSet-class coerce,oGtypeExSet,ExpressionSet-method initialize,oGtypeExSet-method show,oGtypeExSet-method addAnno getSNPindices tx_rsnum
Keywords: classes
Description: Class "oGtypeExSet" ~~~
URL: ../../../library/GGtools/html/oGtypeExSet-class.html

Entry: plot_EvG-methods
Aliases: plot_EvG-methods plot_EvG plot_EvG,genesym,rsNum,smlSet-method getAlleles,smlSet,rsNum-method getAlleles
Keywords: methods
Description: plot expression vs. genotype
URL: ../../../library/GGtools/html/plot_EvG-methods.html

Entry: racExSet-class
Aliases: racExSet-class racExSet genesym-class genesym exFeatID exFeatID-class chr20GGdem gse2031GG hgfocusSYMMEMO mgu74av2SYMMEMO snpID snpID-class getpsid snps,racExSet-method snpNames,racExSet-method racAssays,racExSet-method [,racExSet,ANY,ANY-method oneFit,racExSet-method litsn exclMono oneFit exprs,racExSet-method initialize,racExSet-method litex pdd racAssays snpNames SNPalleles rarebase SNPalleles,racExSet-method rarebase,racExSet-method oneFit,racExSet,genesym,character,function-method oneFit,racExSet,character,character,function-method oneFit,racExSet,list,character,function-method oneFit,racExSet,list,formula,function-method [,racExSet-method [,snpMeta,ANY,ANY,ANY-method [,racExSet,ANY,ANY,ANY-method show,racExSet-method updateObject,racExSet-method snps5PrimeTo snps3PrimeTo snpsNear imputeSNPFixed imputeSNPFixed,racExSet,numeric-method imputeSNPFixed,racExSet,missing-method updateObject,racExSet-method
Keywords: classes
Description: Class "racExSet" for combining RareAlleleCount representations of SNPs, gene expression data, and other phenotype data
URL: ../../../library/GGtools/html/racExSet-class.html

Entry: smlSet-class
Aliases: hmceuB36.2021 smlSet-class chrnum-class rsNum-class [,smlSet-method exprs,smlSet-method nsamp,smlSet-method nsamp rawSNP,smlSet,numeric-method sampleNames,smlSet-method show,smlSet-method smList,smlSet-method smlEnv,smlSet-method getSnpLocs,smlSet-method getSnpLocs,SQLiteConnection,character-method getSnpLocs getSnpChroms,smlSet-method getSnpChroms,SQLiteConnection,character-method getSnpChroms getSnpData getSnpData,character-method rawSNP smList chrnum rsNum chrnum,numeric-method rsNum,character-method getSnpChroms,smlSet,logical-method getSnpChroms,smlSet,missing-method getSnpData,character,character-method getSnpLocs,smlSet,logical-method getSnpLocs,smlSet,missing-method [,smlSet,ANY,ANY-method
Keywords: classes
Description: Class "smlSet" -- efficient representation of SNP+expression data, based on Clayton snpMatrix package
URL: ../../../library/GGtools/html/smlSet-class.html

Entry: snpLocNCref-class
Aliases: snpLocNCref-class getSnpData,snpLocNCref-method show,snpLocNCref-method
Keywords: classes
Description: Class "snpLocNCref" container for netCDF reference to snp location data
URL: ../../../library/GGtools/html/snpLocNCref-class.html

Entry: snpMeta-class
Aliases: snpMeta-class snpMetaWhole-class snpMetaWhole pos pos,snpMeta-method wrapSNPmetaWh chr20meta [,snpMeta-method chromosome,snpMeta-method chromosome coerce,snpMeta,data.frame-method dim,snpMeta-method nrow,snpMeta-method show,snpMeta-method [,snpMeta,ANY,ANY-method
Keywords: classes
Description: Class "snpMeta" -- HapMap (or Wellcome INBREDS) -based metadata structures for SNPs
URL: ../../../library/GGtools/html/snpMeta-class.html

Entry: snpScreen
Aliases: snpScreenResult-class twSnpScreenResult-class show,snpScreenResult-method show,twSnpScreenResult-method annotation,snpScreenResult-method snpScreen,racExSet,snpMeta,genesym,formula,function,numeric-method snpScreen,racExSet,snpMeta,genesym,formula,function,missing-method snpScreen,racExSet,snpMeta,genesym,formula,GGfitter-method twSnpScreen,racExSet,snpMeta,formula,GGfitter-method twSnpScreen snpScreen extract_p plot_mlp
Keywords: models
Description: compute model fits over a sequence of SNPs
URL: ../../../library/GGtools/html/snpScreen.html

Entry: snps
Aliases: snps snps,racExSet,missing-method snps,smlSet,chrnum-method
Keywords: models
Description: accessor for genotype data in a ggExprSet
URL: ../../../library/GGtools/html/snps.html

Entry: topSnps-methods
Aliases: topSnps-methods topSnps topSnps,cwSnpScreenResult-method topSnps,gwSnpScreenResult-method
Keywords: methods
Description: report on the smallest p-values for SNP-expression associations
URL: ../../../library/GGtools/html/topSnps-methods.html
