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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 |
| 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 |
| 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"' |
| 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 |
| 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"' |
| 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 |
| 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 |
| hg19.si.df | software and data for analyses in genetics of gene expression |
| hmm878 | labeled GRanges with ChromHMM chromatin states for GM12878 |
| inflammFilter | functions that compute score tests for all SNP cis to genes, with flexible filtering |
| initialize | Class '"CisConfig"' |
| initialize-method | Class '"CisConfig"' |
| keepMapCache | Class '"CisConfig"' |
| keepMapCache-method | Class '"CisConfig"' |
| keepMapCache<- | Class '"CisConfig"' |
| keepMapCache<--method | Class '"CisConfig"' |
| lgeu | test for variant-expression associations in cis, using VCF |
| locusNames | Class '"transManager"' |
| 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 |
| nperm | Class '"CisConfig"' |
| nperm-method | Class '"CisConfig"' |
| nperm<- | Class '"CisConfig"' |
| nperm<--method | Class '"CisConfig"' |
| nthScores | Class '"transManager"' |
| 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"' |
| 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 |
| 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 |
| 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 |
| 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 |
| update_fdr_filt | support for sensitivity analyses related to eQTL enumerations |
| 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"' |