Entry: GGtools-package
Aliases: GGtools-package GGtools
Keywords: package
Description: GGtools Package Overview
URL: ../../../library/GGtools/html/GGtools-package.html

Entry: aafSNP-class
Aliases: aafSNP-class aafSNP
Keywords: classes
Description: Class "aafSNP" -- container for HTML rendering of SNP metadata
URL: ../../../library/GGtools/html/aafSNP-class.html

Entry: cisSnpTests
Aliases: cisSnpTests
Keywords: models
Description: perform tests for eQTL cis to specified genes
URL: ../../../library/GGtools/html/cisSnpTests.html

Entry: gwSnpTests
Aliases: gwSnpTests residTests residTests,cwSnpScreenResult,smlSet,formula,missing-method chunksize chunksize-class gwSnpTests,formula,smlSet,cnumOrMissing-method gwSnpTests,formula,smlSet,cnumOrMissing,ANY-method gwSnpTests,formula,smlSet,snpdepth-method gwSnpTests,formula,smlSet,snpdepth,ANY-method gwSnpTests,formula,smlSet,snpdepth,chunksize-method
Keywords: models
Description: methods for iterating association tests (expression vs SNP) across genomes or chromosomes
URL: ../../../library/GGtools/html/gwSnpTests.html

Entry: hbTestResults-class
Aliases: hbTestResults-class pvals locs hscores pvals,hbTestResults-method hscores,hbTestResults-method locs,hbTestResults-method
Keywords: classes
Description: Class "hbTestResults" holds results of tests of association of expression levels with haplotype within haplotype block
URL: ../../../library/GGtools/html/hbTestResults-class.html

Entry: hbTests-methods
Aliases: hbTests-methods hbTests hbTests,genesym,smlSet,chrnum,numeric,numeric-method
Keywords: methods
Description: haplotype-block based tests for structured expression variation
URL: ../../../library/GGtools/html/hbTests-methods.html

Entry: hla2set
Aliases: hla2set
Keywords: datasets
Description: a gene set of 9 genes from human HLA2 locus
URL: ../../../library/GGtools/html/hla2set.html

Entry: hmceuB36.2021
Aliases: hmceuB36.2021
Keywords: datasets
Description: two chromosomes of genotype data and full expression data for CEPH CEU hapmap data
URL: ../../../library/GGtools/html/hmceuB36.2021.html

Entry: invokePhase-methods
Aliases: invokePhase invokePhase-methods invokePhase,phaseInput,chrnum,character,character,character,logical-method invokePhase,snp.matrix,chrnum,character,character,character,logical-method
Keywords: methods
Description: ~~ Methods for Function invokePhase in Package 'GGtools' ~~
URL: ../../../library/GGtools/html/invokePhase-methods.html

Entry: masterSnps
Aliases: masterSnps
Keywords: models
Description: visualize a multiGwSnpScreenResult
URL: ../../../library/GGtools/html/masterSnps.html

Entry: plot-methods
Aliases: plot,cwSnpScreenResult,missing-method plot,filteredGwSnpScreenResult,ANY-method plot,filteredMultiGwSnpScreenResult,ANY-method plot,snp.reg.imputation,missing-method
Keywords: methods
Description: Methods for Function plot in Package 'GGtools'
URL: ../../../library/GGtools/html/plot-methods.html

Entry: snpm2mapLD
Aliases: snpm2mapLD smtest
Keywords: models
Description: prepare input to mapLD function for haplotype block identification
URL: ../../../library/GGtools/html/snpm2mapLD.html

Entry: snpm2phase
Aliases: snpm2phase parsePh.out personalHap phaseInput-class
Keywords: models
Description: convert information in a snp.matrix to PHASE input format; invokePhase can run a suitably installed version of PHASE
URL: ../../../library/GGtools/html/snpm2phase.html

Entry: strMultPop
Aliases: strMultPop
Keywords: datasets
Description: serialization of a table from Stringer's multipopulation eQTL report
URL: ../../../library/GGtools/html/strMultPop.html

Entry: topSnps-methods
Aliases: topSnps topSnps-methods topSnps,cwSnpScreenResult-method topSnps,gwSnpScreenResult-method
Keywords: methods
Description: report on most significant SNP with gwSnpTests results
URL: ../../../library/GGtools/html/topSnps-methods.html

Entry: GGtools-RangedData
Aliases: coerce,cwSnpScreenResult,RangedData-method
Keywords: methods
Description: Transform results of gwSnpTests to browser tracks
URL: ../../../library/GGtools/html/trackSet-methods.html
