software and data for analyses in genetics of gene expression


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Documentation for package ‘GGtools’ version 5.6.0

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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
addgwhit functions that compute score tests for all SNP cis to genes, with flexible filtering
All.cis functions that compute score tests for all SNP cis to genes, with flexible filtering
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
bindgwava appraisal for eQTL prediction models
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 Class '"EqAppr"'
calfig-method Class '"EqAppr"'
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
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 test for variant-expression associations in cis, using 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
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 --

EqAppr-class Class '"EqAppr"'
eqBox descriptive plot of expression against genotype for cisAssoc results
eqDesc descriptive plot of expression against genotype for cisAssoc results
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
getModnames-method Class '"EqAppr"'
getPruned-method Class '"EqAppr"'
getSens-method Class '"EqAppr"'
getUnpruned-method Class '"EqAppr"'
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
initialize Class '"CisConfig"'
initialize-method Class '"CisConfig"'

-- K --

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

-- L --

lgeu test for variant-expression associations in cis, using VCF
locusNames Class '"transManager"'

-- M --

mcwAllCis-class functions that compute score tests for all SNP cis to genes, with flexible filtering
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
show-method Class '"CisConfig"'
show-method Class '"EqAppr"'
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"'