# software and data for genetical genomics (c) 2006 VJ Carey

## Documentation for package ‘GGtools’ version 3.4.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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