Man pages for Bioconductor-mirror/GGtools
software and data for analyses in genetics of gene expression

All.cisfunctions that compute score tests for all SNP cis to genes,...
appraiseappraisal for eQTL prediction models
b1mcwBestCis instances, integrative analysis output containers...
best.cis.eQTLscollect genewise best scoring eQTL
best.trans.eQTLscollect strongest trans SNP-gene associations in a buffer of...
bindmafbind testing metadata to a best.cis.eQTLs result
cgff2dttranslate the GFF3 from a ciseqByCluster/processgff output...
cisAssoctest for variant-expression associations in cis, using VCF
CisConfig-classClass '"CisConfig"'
ciseqByClusterend-to-end cluster-based cis-eQTL search, and allied...
cisRun-classClass '"cisRun"'
collectBestgiven a collection of All.cis outputs (cisRun instances)...
concatCiscombine a list of cisRun instances to a single instance
EqAppr-classClass '"EqAppr"'
eqBoxdescriptive plot of expression against genotype for cisAssoc...
eqsens_dtsupport for sensitivity analyses related to eQTL enumerations
eqtlTestscompute association statistics between all probes and SNP in...
eqtlTestsManager-classClass '"eqtlTestsManager"'
eqtlTests.meuse MatrixEQTL computations and statistics as a back end to...
exExpressionSet instance for illustrating integrative smlSet...
getCisMapcreate, using Bioconductor annotation resources, a structure...
gffprocesstransform a collection of gff3 into a single tabix-indexed...
GGtools-packagesoftware and data for analyses in genetics of gene expression
gwSnpTestsexecute a series of tests for association between genotype...
hmm878labeled GRanges with ChromHMM chromatin states for GM12878
pifdrutility for computing plug-in FDR
qqhexobtain qqplot coordinates for the specific case of comparing...
richNullbind metadata concerning SNP allele frequency and other...
sampsInVCFenumerate samples available in a VCF file
scoresCisvisualize a gene model with cis-eQTL association scores (-log...
sensanalSummarize information from a collection of eQTL searches for...
sensiCisInput-classClass '"sensiCisInput"'
sensiCisOutput-classClass '"sensiCisOutput"'
simpleTilingcreate a GRanges with a tiling of the human genome
snplocsDefaultname the default SNPlocs.Hsapiens.dbSNP.* package
strMultPopserialization of a table from Stranger's multipopulation eQTL...
TransConfig-classClass '"TransConfig"'
transeqByClusterconvenience functions for trans-eQTL testing
transManager-classClass '"transManager"'
transScoresobtain the top trans associations for each SNP in an smlSet
transTabtabulate results of transScores run
vcf2smgenerate a SnpMatrix instance on the basis of a VCF (4.0)...
Bioconductor-mirror/GGtools documentation built on June 23, 2017, 2:16 p.m.