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| GGtools-package | GGtools Package Overview |
| aafSNP | Class "aafSNP" - container for HTML rendering of SNP metadata |
| aafSNP-class | Class "aafSNP" - container for HTML rendering of SNP metadata |
| chunksize | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| chunksize-class | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| cisSnpTests | perform tests for eQTL cis to specified genes |
| coerce,cwSnpScreenResult,RangedData-method | Transform results of gwSnpTests to browser tracks |
| GGtools | GGtools Package Overview |
| gwSnpTests | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| gwSnpTests,formula,smlSet,cnumOrMissing,ANY-method | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| gwSnpTests,formula,smlSet,cnumOrMissing,missing-method | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| gwSnpTests,formula,smlSet,cnumOrMissing-method | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| gwSnpTests,formula,smlSet,snpdepth,ANY-method | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| gwSnpTests,formula,smlSet,snpdepth,chunksize-method | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| gwSnpTests,formula,smlSet,snpdepth,missing-method | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| gwSnpTests,formula,smlSet,snpdepth-method | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| hbTestResults-class | Class "hbTestResults" holds results of tests of association of expression levels with haplotype within haplotype block |
| hbTests | haplotype-block based tests for structured expression variation |
| hbTests,genesym,smlSet,chrnum,numeric,numeric-method | haplotype-block based tests for structured expression variation |
| hbTests-methods | haplotype-block based tests for structured expression variation |
| hla2set | a gene set of 9 genes from human HLA2 locus |
| hmceuB36.2021 | two chromosomes of genotype data and full expression data for CEPH CEU hapmap data |
| hscores | Class "hbTestResults" holds results of tests of association of expression levels with haplotype within haplotype block |
| hscores,hbTestResults-method | Class "hbTestResults" holds results of tests of association of expression levels with haplotype within haplotype block |
| invokePhase | ~~ Methods for Function invokePhase in Package 'GGtools' ~~ |
| invokePhase,phaseInput,chrnum,character,character,character,logical-method | ~~ Methods for Function invokePhase in Package 'GGtools' ~~ |
| invokePhase,snp.matrix,chrnum,character,character,character,logical-method | ~~ Methods for Function invokePhase in Package 'GGtools' ~~ |
| invokePhase-methods | ~~ Methods for Function invokePhase in Package 'GGtools' ~~ |
| locs | Class "hbTestResults" holds results of tests of association of expression levels with haplotype within haplotype block |
| locs,hbTestResults-method | Class "hbTestResults" holds results of tests of association of expression levels with haplotype within haplotype block |
| make_smlSet | create an smlSet instance from components |
| masterSnps | visualize a multiGwSnpScreenResult |
| parsePh.out | convert information in a snp.matrix to PHASE input format; invokePhase can run a suitably installed version of PHASE |
| personalHap | convert information in a snp.matrix to PHASE input format; invokePhase can run a suitably installed version of PHASE |
| phaseInput-class | convert information in a snp.matrix to PHASE input format; invokePhase can run a suitably installed version of PHASE |
| plot,cwSnpScreenResult,missing-method | Methods for Function plot in Package 'GGtools' |
| plot,filteredGwSnpScreenResult,ANY-method | Methods for Function plot in Package 'GGtools' |
| plot,filteredMultiGwSnpScreenResult,ANY-method | Methods for Function plot in Package 'GGtools' |
| plot,snp.reg.imputation,missing-method | Methods for Function plot in Package 'GGtools' |
| pvals | Class "hbTestResults" holds results of tests of association of expression levels with haplotype within haplotype block |
| pvals,hbTestResults-method | Class "hbTestResults" holds results of tests of association of expression levels with haplotype within haplotype block |
| residTests | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| residTests,cwSnpScreenResult,smlSet,formula,missing-method | methods for iterating association tests (expression vs SNP) across genomes or chromosomes |
| smtest | prepare input to mapLD function for haplotype block identification |
| snpm2mapLD | prepare input to mapLD function for haplotype block identification |
| snpm2phase | convert information in a snp.matrix to PHASE input format; invokePhase can run a suitably installed version of PHASE |
| strMultPop | serialization of a table from Stringer's multipopulation eQTL report |
| topSnps | report on most significant SNP with gwSnpTests results |
| topSnps,cwSnpScreenResult-method | report on most significant SNP with gwSnpTests results |
| topSnps,gwSnpScreenResult-method | report on most significant SNP with gwSnpTests results |
| topSnps-methods | report on most significant SNP with gwSnpTests results |