GGtools-package |
software and data for analyses in genetics of gene expression |
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 |
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"' |
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.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"' |
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 '"transManager"' |
show-method |
generate a SnpMatrix instance on the basis of a VCF (4.0) file |
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"' |