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; new cisAssoc works with SummarizedExperiment and VCF |
addgwhit | functions that compute score tests for all SNP cis to genes, with flexible filtering; new cisAssoc works with SummarizedExperiment and VCF |
All.cis | functions that compute score tests for all SNP cis to genes, with flexible filtering; new cisAssoc works with SummarizedExperiment and VCF |
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 |
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 | plot results of appraise to exhibit model calibration |
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; new cisAssoc works with SummarizedExperiment and VCF |
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 | functions that compute score tests for all SNP cis to genes, with flexible filtering; new cisAssoc works with SummarizedExperiment and 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; new cisAssoc works with SummarizedExperiment and VCF |
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 |
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 |
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; new cisAssoc works with SummarizedExperiment and VCF |
initialize | Class '"CisConfig"' |
initialize-method | Class '"CisConfig"' |
keepMapCache | Class '"CisConfig"' |
keepMapCache-method | Class '"CisConfig"' |
keepMapCache<- | Class '"CisConfig"' |
keepMapCache<--method | Class '"CisConfig"' |
locusNames | Class '"transManager"' |
mcwAllCis-class | functions that compute score tests for all SNP cis to genes, with flexible filtering; new cisAssoc works with SummarizedExperiment and VCF |
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; new cisAssoc works with SummarizedExperiment and VCF |
show-method | Class '"CisConfig"' |
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"' |