# software and data for analyses in genetics of gene expression

## Documentation for package ‘GGtools’ version 4.4.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

GGtools-package | software and data for analyses in genetics of gene expression
All.cis.eQTLs | collect genewise best scoring eQTL
allSigCis-class | collect genewise best scoring eQTL
best.cis.eQTLs | collect genewise best scoring eQTL
chromsUsed | collect genewise best scoring eQTL
chromsUsed-method | collect genewise best scoring eQTL
eqtlEstimates | compute association statistics between all probes and SNP in an smlSet instance
eqtlEstimatesManager-class | Class '"eqtlTestsManager"'
eqtlTests | compute association statistics between all probes and SNP in an smlSet instance
eqtlTestsManager-class | Class '"eqtlTestsManager"'
ex | ExpressionSet instance for illustrating integrative smlSet container
fdr | collect genewise best scoring eQTL
fullreport | collect genewise best scoring eQTL
fullreport-method | collect genewise best scoring eQTL
geneIndcol | Class '"transManager"'
geneNames | Class '"transManager"'
getAll | collect genewise best scoring eQTL
getBest | collect genewise best scoring eQTL
getCall | collect genewise best scoring eQTL
getCisMap | create, using Bioconductor annotation resources, a structure that enumerates SNP in the vicinity of ('cis' to) genes
GGtools | software and data for analyses in genetics of gene expression
gwSnpScreenResult-class | execute a series of tests for association between genotype and expression
gwSnpTests | execute a series of tests for association between genotype and expression
gwSnpTests-method | execute a series of tests for association between genotype and expression
locusNames | Class '"transManager"'
mcwBestCis-class | collect genewise best scoring eQTL
meqtlTests | compute association statistics between all probes and SNP in an smlSet instance
meta.All.cis.eQTLs | collect genewise best scoring eQTL
meta.best.cis.eQTLs | collect genewise best scoring eQTL
mtransScores | obtain the top trans associations for each SNP in an smlSet
nthScores | Class '"transManager"'
plot-method | execute a series of tests for association between genotype and expression
probesManaged | Class '"eqtlTestsManager"'
show-method | collect genewise best scoring eQTL
show-method | Class '"eqtlTestsManager"'
show-method | create, using Bioconductor annotation resources, a structure that enumerates SNP in the vicinity of ('cis' to) genes
show-method | execute a series of tests for association between genotype and expression
show-method | Class '"transManager"'
show-method | generate a SnpMatrix instance on the basis of a VCF (4.0) file
snpsManaged | Class '"eqtlTestsManager"'
strMultPop | serialization of a table from Stranger's multipopulation eQTL report
topFeats | Class '"eqtlTestsManager"'
topFeats-method | Class '"eqtlTestsManager"'
topGenes | Class '"transManager"'
topScores | Class '"transManager"'
topSnps | execute a series of tests for association between genotype and expression
topSnps-method | execute a series of tests for association between genotype and expression
tr1_obs | obtain the top trans associations for each SNP in an smlSet
tr1_perm | obtain the top trans associations for each SNP in an smlSet
transManager-class | Class '"transManager"'
transScores | obtain the top trans associations for each SNP in an smlSet
transTab | tabulate results of transScores run
transTab-method | Class '"transManager"'
vcf2sm | generate a SnpMatrix instance on the basis of a VCF (4.0) file
vcf2sm-method | generate a SnpMatrix instance on the basis of a VCF (4.0) file
[-method | Class '"eqtlTestsManager"'