API for RTN
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Global functions
.alpha.adjust Source code
.annotate.regulons.gsea2 Source code
.annotate.regulons.hypergeo Source code
.annotate.regulons.jaccard Source code
.annotate.samples.gsea Source code
.avs.checks Source code
.barplot.pos.vs.neg Source code
.bcpower Source code
.boxcox.adj Source code
.edf.pos.vs.neg Source code
.estimate.bcpower Source code
.expDataChecks Source code
.fgseaScores4TNI Source code
.get.regulon.summary Source code
.get.tnet.summary Source code
.gmm.scores Source code
.gmmlist Source code
.gsea2.target.contribution Source code
.hclust2igraph Source code
.hyperGeoTest4RTN Source code
.hypergeo.genesets Source code
.isUnloggedData Source code
.jaccard.genesets Source code
.log2transform Source code
.mi2gmm.dpi Source code
.mi2gmm.ref Source code
.mtdata Source code
.perm.pmin.pooled Source code
.perm.pmin.separate Source code
.points.pos.vs.neg Source code
.preprocess.genesets Source code
.regulon.summary Source code
.regulonCounts Source code
.regulonGroupFET Source code
.run.tni.gsea1.alternative Source code
.run.tni.gsea2.alternative Source code
.target.contribution Source code
.tni.stratification.area Source code
.tni.stratification.gsea2 Source code
.update_pEVSE Source code
AVS-class Man page
RTN Man page
RTN-package Man page
TNA-class Man page
TNI-class Man page
all.binaryValues Source code
all.characterValues Source code
all.integerValues Source code
avs.evse Man page
avs.evse,AVS-method Man page
avs.get Man page
avs.get,AVS-method Man page
avs.pevse Man page
avs.pevse,AVS-method Man page
avs.plot1 Man page Source code
avs.plot2 Man page Source code
avs.vse Man page
avs.vse,AVS-method Man page
avsplot1 Source code
avsplot2 Source code
cdt.list Source code
cdt.stability Source code
cdt.table Source code
check.format1 Source code
check.format2 Source code
checkModuationEffect Source code
checkTars Source code
cv.filter Source code
data.integration Source code
eqtlExtract Source code
eqtlExtractAnova Source code
eqtlExtractFull Source code
eqtlTest Source code
eqtlTestDetailed Source code
eqtlTestDetailedAnova Source code
evsea Source code
evseaproxy Source code
expressionCorrelation Source code
get.avsdist Source code
get.eqtldist Source code
get.merged.data1 Source code
get.merged.data2 Source code
get.pre_eqtldist Source code
getAnnotOverlap1 Source code
getAnnotOverlap2 Source code
getAnnotRanges Source code
getAvsRanges Source code
getEvseEqtls Source code
getEvseMatrix Source code
getMappedClusters Source code
getMappedMarkers Source code
getMarkers.rset Source code
getMarkers.vset Source code
getRandomAvsRanges Source code
getUniverseCounts1 Source code
getUniverseCounts2 Source code
gettfs Source code
gsea1tna Source code
gsea2tna Source code
gseaScores4RTN Source code
gseaScoresBatch4RTN Source code
gsplot1 Source code
gsplot2 Source code
hcEdges.filter Source code
hclust2igraph Source code
hits.preprocess Source code
hyperGeoTest4RTN Source code
is.color Source code
is.singleInteger Source code
is.singleLogical Source code
is.singleNumber Source code
is.singleString Source code
isParallel Source code
make.plot1 Source code
make.plot2 Source code
maprset Source code
mapvset Source code
miMdTfStats Source code
miThresholdMd Source code
miThresholdMdTf Source code
mutualInformation Source code
p.adjust.cdt.list Source code
p.adjust.cdt.table Source code
p.format.cdt.table Source code
pheno.preprocess Source code
pksData Man page
plot.gsea1 Source code
plot.gsea2 Source code
pre_evsea Source code
report.vset Source code
run.gsea1 Source code
run.gsea2 Source code
setregs1 Source code
setregs2 Source code
shtest Source code
sortAnnotation Source code
sortblock.cdt.list Source code
stni Man page
tfsData Man page
tna.duplicate.remover Source code
tna.get Man page
tna.get,TNA-method Man page
tna.gsea1 Man page
tna.gsea1,TNA-method Man page
tna.gsea2 Man page
tna.gsea2,TNA-method Man page
tna.mra Man page
tna.mra,TNA-method Man page
tna.perm.pvalues Source code
tna.plot.gsea1 Man page Source code
tna.plot.gsea2 Man page Source code
tna.preprocess Source code
tnaData Man page
tnai.checks Source code
tni.alpha.adjust Man page Source code
tni.amap Source code
tni.annotate.regulons Man page
tni.annotate.regulons,TNI-method Man page
tni.annotate.samples Man page
tni.annotate.samples,TNI-method Man page
tni.area3 Man page
tni.area3,TNI-method Man page
tni.boot Source code
tni.bootstrap Man page
tni.bootstrap,TNI-method Man page
tni.conditional Man page
tni.conditional,TNI-method Man page
tni.constructor Man page Source code
tni.cor Source code
tni.dpi Source code
tni.dpi.filter Man page
tni.dpi.filter,TNI-method Man page
tni.get Man page
tni.get,TNI-method Man page
tni.graph Man page
tni.graph,TNI-method Man page
tni.gsea2 Man page
tni.gsea2,TNI-method Man page
tni.mmap Source code
tni.mmap.detailed Source code
tni.overlap.genesets Man page
tni.overlap.genesets,TNI-method Man page
tni.perm.pooled Source code
tni.perm.separate Source code
tni.permutation Man page
tni.permutation,TNI-method Man page
tni.phyper Source code
tni.plot.checks Man page Source code
tni.plot.sre Man page Source code
tni.pmin Source code
tni.preprocess Man page
tni.preprocess,TNI-method Man page
tni.prune Man page
tni.prune,TNI-method Man page
tni.regulon.summary Man page
tni.regulon.summary,TNI-method Man page
tni.replace.samples Man page
tni.replace.samples,TNI-method Man page
tni.rmap Source code
tni.sre Man page
tni.sre,TNI-method Man page
tni2tna.preprocess Man page
tni2tna.preprocess,TNI-method Man page
tniData Man page
translateQuery Source code
treemap Source code
upgradeTNA Man page Source code
upgradeTNI Man page Source code
vsea Source code
vseformat Source code
vsereport Source code
RTN documentation built on Nov. 12, 2020, 2:02 a.m.