# software and data for analyses in genetics of gene expression

## Documentation for package ‘GGtools’ version 5.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C E F G H I K L M N P Q R S T U V misc

GGtools-package | software and data for analyses in genetics of gene expression

## -- A --

add878 | functions that compute score tests for all SNP cis to genes, with flexible filtering; new cisAssoc works with SummarizedExperiment and VCF
addgwhit | functions that compute score tests for all SNP cis to genes, with flexible filtering; new cisAssoc works with SummarizedExperiment and VCF
All.cis | functions that compute score tests for all SNP cis to genes, with flexible filtering; new cisAssoc works with SummarizedExperiment and VCF
All.cis.eQTLs | collect genewise best scoring eQTL
allSigCis-class | collect genewise best scoring eQTL
appraise | appraisal for eQTL prediction models

## -- B --

b1 | mcwBestCis instances, integrative analysis output containers generated by GGtools vignette
b2 | mcwBestCis instances, integrative analysis output containers generated by GGtools vignette
batchsize | Class '"TransConfig"'
batchsize-method | Class '"TransConfig"'
batchsize<- | Class '"TransConfig"'
batchsize<--method | Class '"TransConfig"'
best.cis.eQTLs | collect genewise best scoring eQTL
best.trans.eQTLs | collect strongest trans SNP-gene associations in a buffer of size K genes per SNP
binnedQQ | obtain qqplot coordinates for the specific case of comparing a given distribution to that of multiple realizations from a permutation distribution, and bin these coordinates using hexbin, useful for very large samples
binqq | obtain qqplot coordinates for the specific case of comparing a given distribution to that of multiple realizations from a permutation distribution, and bin these coordinates using hexbin, useful for very large samples
buildConfList | Class '"CisConfig"'

## -- C --

calfig | plot results of appraise to exhibit model calibration
cgff2dt | translate the GFF3 from a ciseqByCluster/processgff output into a serialized data.table instance, compute genome-wide plug-in FDR, and update the GFF3 with this FDR
chrFilter | functions that compute score tests for all SNP cis to genes, with flexible filtering; new cisAssoc works with SummarizedExperiment and VCF
chrnames | Class '"CisConfig"'
chrnames-method | Class '"CisConfig"'
chrnames<- | Class '"CisConfig"'
chrnames<--method | Class '"CisConfig"'
chromsUsed | collect genewise best scoring eQTL
chromsUsed-method | collect genewise best scoring eQTL
cis.FDR.filter.best | given a collection of All.cis outputs (cisRun instances) compute FDRs for various filterings
cis.FDR.filter.SNPcentric | given a collection of All.cis outputs (cisRun instances) compute FDRs for various filterings
cis.FDR.filter.SNPcentric.complete | given a collection of All.cis outputs (cisRun instances) compute FDRs for various filterings
cisAssoc | functions that compute score tests for all SNP cis to genes, with flexible filtering; new cisAssoc works with SummarizedExperiment and VCF
CisConfig-class | Class '"CisConfig"'
ciseqByCluster | end-to-end cluster-based cis-eQTL search, and allied utilities
cisRun-class | Class '"cisRun"'
cisScores | functions that compute score tests for all SNP cis to genes, with flexible filtering; new cisAssoc works with SummarizedExperiment and VCF
collectBest | given a collection of All.cis outputs (cisRun instances) compute FDRs for various filterings
collectFiltered | given a collection of All.cis outputs (cisRun instances) compute FDRs for various filterings
concatCis | combine a list of cisRun instances to a single instance

## -- E --

eqsens_dt | support for sensitivity analyses related to eQTL enumerations
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
eqtlTests.me | use MatrixEQTL computations and statistics as a back end to GGtools eqtlTests
eqtlTestsManager-class | Class '"eqtlTestsManager"'
estimates | Class '"CisConfig"'
estimates-method | Class '"CisConfig"'
estimates<- | Class '"CisConfig"'
estimates<--method | Class '"CisConfig"'
ex | ExpressionSet instance for illustrating integrative smlSet container
excludeRadius | Class '"CisConfig"'
excludeRadius-method | Class '"CisConfig"'
excludeRadius<- | Class '"CisConfig"'
excludeRadius<--method | Class '"CisConfig"'
exFilter | Class '"CisConfig"'
exFilter-method | Class '"CisConfig"'
exFilter<- | Class '"CisConfig"'
exFilter<--method | Class '"CisConfig"'
extraProps | Class '"CisConfig"'
extraProps-method | Class '"CisConfig"'
extraProps<- | Class '"CisConfig"'
extraProps<--method | Class '"CisConfig"'

## -- F --

fdr | collect genewise best scoring eQTL
filtgen.maf.dist | support for sensitivity analyses related to eQTL enumerations
folderStem | Class '"CisConfig"'
folderStem-method | Class '"CisConfig"'
folderStem<- | Class '"CisConfig"'
folderStem<--method | Class '"CisConfig"'
fullreport | collect genewise best scoring eQTL
fullreport-method | collect genewise best scoring eQTL

## -- G --

gbufsize | Class '"TransConfig"'
gbufsize-method | Class '"TransConfig"'
gbufsize<- | Class '"TransConfig"'
gbufsize<--method | Class '"TransConfig"'
gchrpref | Class '"CisConfig"'
gchrpref-method | Class '"CisConfig"'
gchrpref<- | Class '"CisConfig"'
gchrpref<--method | Class '"CisConfig"'
geneannopk | Class '"CisConfig"'
geneannopk-method | Class '"CisConfig"'
geneannopk<- | Class '"CisConfig"'
geneannopk<--method | Class '"CisConfig"'
geneApply | Class '"CisConfig"'
geneApply-method | Class '"CisConfig"'
geneApply<- | Class '"CisConfig"'
geneApply<--method | Class '"CisConfig"'
geneIndcol | Class '"transManager"'
geneNames | Class '"transManager"'
genome | Class '"CisConfig"'
genome-method | Class '"CisConfig"'
genome<- | Class '"CisConfig"'
genome<--method | Class '"CisConfig"'
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
gffprocess | transform a collection of gff3 into a single tabix-indexed gff3
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

## -- H --

hg19.si.df | software and data for analyses in genetics of gene expression
hmm878 | labeled GRanges with ChromHMM chromatin states for GM12878

## -- I --

inflammFilter | functions that compute score tests for all SNP cis to genes, with flexible filtering; new cisAssoc works with SummarizedExperiment and VCF
initialize | Class '"CisConfig"'
initialize-method | Class '"CisConfig"'

## -- K --

keepMapCache | Class '"CisConfig"'
keepMapCache-method | Class '"CisConfig"'
keepMapCache<- | Class '"CisConfig"'
keepMapCache<--method | Class '"CisConfig"'

## -- L --

locusNames | Class '"transManager"'

## -- M --

mcwAllCis-class | functions that compute score tests for all SNP cis to genes, with flexible filtering; new cisAssoc works with SummarizedExperiment and VCF
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
meta.bindmaf | bind testing metadata to a best.cis.eQTLs result
meta.richNull | bind metadata concerning SNP allele frequency and other aspects of optimized cis-eQTL association to an mcwBestCis instance
meta.transScores | obtain the top trans associations for each SNP in an smlSet
mtransScores | obtain the top trans associations for each SNP in an smlSet

## -- N --

nperm | Class '"CisConfig"'
nperm-method | Class '"CisConfig"'
nperm<- | Class '"CisConfig"'
nperm<--method | Class '"CisConfig"'
nthScores | Class '"transManager"'

## -- P --

pifdr | utility for computing plug-in FDR
plot-method | execute a series of tests for association between genotype and expression
plotsens | support for sensitivity analyses related to eQTL enumerations
probesManaged | Class '"eqtlTestsManager"'

## -- Q --

qqhex | obtain qqplot coordinates for the specific case of comparing a given distribution to that of multiple realizations from a permutation distribution, and bin these coordinates using hexbin, useful for very large samples

## -- R --

radius | Class '"CisConfig"'
radius-method | Class '"CisConfig"'
radius<- | Class '"CisConfig"'
radius<--method | Class '"CisConfig"'
rhs | Class '"CisConfig"'
rhs-method | Class '"CisConfig"'
rhs<- | Class '"CisConfig"'
rhs<--method | Class '"CisConfig"'
richNull | bind metadata concerning SNP allele frequency and other aspects of optimized cis-eQTL association to an mcwBestCis instance

## -- S --

sampsInVCF | enumerate samples available in a VCF file
schrpref | Class '"CisConfig"'
schrpref-method | Class '"CisConfig"'
schrpref<- | Class '"CisConfig"'
schrpref<--method | Class '"CisConfig"'
scoresCis | visualize a gene model with cis-eQTL association scores (-log FDR by default) on the basis of a ciseqByCluster data.table output
sensanal | Summarize information from a collection of eQTL searches for sensitivity assessment
sensanal-method | Class '"sensiCisInput"'
sensiCisInput-class | Class '"sensiCisInput"'
sensiCisOutput-class | Class '"sensiCisOutput"'
shortfac | Class '"CisConfig"'
shortfac-method | Class '"CisConfig"'
shortfac<- | Class '"CisConfig"'
shortfac<--method | Class '"CisConfig"'
show | Class '"CisConfig"'
show-method | functions that compute score tests for all SNP cis to genes, with flexible filtering; new cisAssoc works with SummarizedExperiment and VCF
show-method | Class '"CisConfig"'
show-method | Class '"TransConfig"'
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 '"sensiCisInput"'
show-method | Class '"sensiCisOutput"'
show-method | Class '"transManager"'
show-method | generate a SnpMatrix instance on the basis of a VCF (4.0) file
simpleTiling | create a GRanges with a tiling of the human genome
smchrpref | Class '"CisConfig"'
smchrpref-method | Class '"CisConfig"'
smchrpref<- | Class '"CisConfig"'
smchrpref<--method | Class '"CisConfig"'
smFilter | Class '"CisConfig"'
smFilter-method | Class '"CisConfig"'
smFilter<- | Class '"CisConfig"'
smFilter<--method | Class '"CisConfig"'
smpack | Class '"CisConfig"'
smpack-method | Class '"CisConfig"'
smpack<- | Class '"CisConfig"'
smpack<--method | Class '"CisConfig"'
snpannopk | Class '"CisConfig"'
snpannopk-method | Class '"CisConfig"'
snpannopk<- | Class '"CisConfig"'
snpannopk<--method | Class '"CisConfig"'
snpchr | Class '"TransConfig"'
snpchr-method | Class '"TransConfig"'
snpchr<- | Class '"TransConfig"'
snpchr<--method | Class '"TransConfig"'
snplocsDefault | name the default SNPlocs.Hsapiens.dbSNP.* package
snpsManaged | Class '"eqtlTestsManager"'
SSgen | Class '"CisConfig"'
SSgen-method | Class '"CisConfig"'
SSgen<- | Class '"CisConfig"'
SSgen<--method | Class '"CisConfig"'
strMultPop | serialization of a table from Stranger's multipopulation eQTL report

## -- T --

TabixFile | enumerate samples available in a VCF file
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
TransConfig-class | Class '"TransConfig"'
transeqByChrom | convenience functions for trans-eQTL testing
transeqByCluster | convenience functions for trans-eQTL testing
transManager-class | Class '"transManager"'
transScores | obtain the top trans associations for each SNP in an smlSet
transScores.legacy | obtain the top trans associations for each SNP in an smlSet
transTab | tabulate results of transScores run
transTab-method | tabulate results of transScores run

## -- U --

update_fdr_filt | support for sensitivity analyses related to eQTL enumerations

## -- V --

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

## -- misc --

[-method | Class '"eqtlTestsManager"'