| All.cis | functions that compute score tests for all SNP cis to genes,... |
| appraise | appraisal for eQTL prediction models |
| b1 | mcwBestCis instances, integrative analysis output containers... |
| best.cis.eQTLs | collect genewise best scoring eQTL |
| best.trans.eQTLs | collect strongest trans SNP-gene associations in a buffer of... |
| bindmaf | bind testing metadata to a best.cis.eQTLs result |
| cgff2dt | translate the GFF3 from a ciseqByCluster/processgff output... |
| 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... |
| cisRun-class | Class '"cisRun"' |
| collectBest | given a collection of All.cis outputs (cisRun instances)... |
| concatCis | combine a list of cisRun instances to a single instance |
| EqAppr-class | Class '"EqAppr"' |
| eqBox | descriptive plot of expression against genotype for cisAssoc... |
| eqsens_dt | support for sensitivity analyses related to eQTL enumerations |
| eqtlTests | compute association statistics between all probes and SNP in... |
| eqtlTestsManager-class | Class '"eqtlTestsManager"' |
| eqtlTests.me | use MatrixEQTL computations and statistics as a back end to... |
| ex | ExpressionSet instance for illustrating integrative smlSet... |
| getCisMap | create, using Bioconductor annotation resources, a structure... |
| gffprocess | transform a collection of gff3 into a single tabix-indexed... |
| GGtools-package | software and data for analyses in genetics of gene expression |
| gwSnpTests | execute a series of tests for association between genotype... |
| hmm878 | labeled GRanges with ChromHMM chromatin states for GM12878 |
| pifdr | utility for computing plug-in FDR |
| qqhex | obtain qqplot coordinates for the specific case of comparing... |
| richNull | bind metadata concerning SNP allele frequency and other... |
| sampsInVCF | enumerate samples available in a VCF file |
| scoresCis | visualize a gene model with cis-eQTL association scores (-log... |
| sensanal | Summarize information from a collection of eQTL searches for... |
| sensiCisInput-class | Class '"sensiCisInput"' |
| sensiCisOutput-class | Class '"sensiCisOutput"' |
| simpleTiling | create a GRanges with a tiling of the human genome |
| snplocsDefault | name the default SNPlocs.Hsapiens.dbSNP.* package |
| strMultPop | serialization of a table from Stranger's multipopulation eQTL... |
| TransConfig-class | Class '"TransConfig"' |
| transeqByCluster | convenience functions for trans-eQTL testing |
| transManager-class | Class '"transManager"' |
| transScores | obtain the top trans associations for each SNP in an smlSet |
| transTab | tabulate results of transScores run |
| vcf2sm | generate a SnpMatrix instance on the basis of a VCF (4.0)... |
