software and data for analyses in genetics of gene expression

[Up] [Top]

Documentation for package ‘GGtools’ version 4.8.0

Help Pages

GGtools-package software and data for analyses in genetics of gene expression
All.cis function that computes 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
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
bindmaf bind testing metadata to a best.cis.eQTLs result
chrFilter function that computes score tests for all SNP cis to genes, with flexible filtering
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"'
mcwAllCis-class function that computes 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
nthScores Class '"transManager"'
plot-method execute a series of tests for association between genotype and expression
probesManaged Class '"eqtlTestsManager"'
richNull bind metadata concerning SNP allele frequency and other aspects of optimized cis-eQTL association to an mcwBestCis instance
sensanal Summarize information from a collection of eQTL searches for sensitivity assessment
sensanal-method Class '"sensiCisInput"'
sensiCisInput-class Class '"sensiCisInput"'
sensiCisOutput-class Class '"sensiCisOutput"'
show-method function that computes score tests for all SNP cis to genes, with flexible filtering
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
snplocsDefault name the default SNPlocs.Hsapiens.dbSNP.* package
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 tabulate results of transScores run
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"'