API for wuaipinglab/sitePath
Phylogenetic pathway–dependent recognition of fixed substitutions and parallel mutations

Global functions
.actualExtractSite Source code
.annotateSNPonTree Source code
.assignClusterNames Source code
.calibrateFixedAA Source code
.calibrateNode Source code
.checkSite Source code
.childrenTips Source code
.clusterByFixation Source code
.collectParallelSites Source code
.createCluster Source code
.createSNPplot Source code
.findAncestralNode Source code
.findFixationPath Source code
.findGroupingLinkage Source code
.groupMutationsBySites Source code
.mergeClusters Source code
.mutationTable Source code
.pathsUnderThreshold Source code
.phyMSAmatch Source code
.qualifiedFixation Source code
.qualifiedMutAA Source code
.runEntropyMinimization Source code
.selectMutByAA Source code
.siteColorScheme Source code
.stablePathIndex Source code
.tipSeqsAlongPathNodes Source code
.unambiguousChars Source code
.unifyEntropyGrouping Source code
.unpackClustersByPath Source code
SNPsites Man page Source code
SNPsites.phyMSAmatched Man page Source code
addMSA Man page Source code
addMSA.phylo Man page Source code
addMSA.treedata Man page Source code
allSitesName Man page Source code
allSitesName.SNPsites Man page Source code
allSitesName.fixationSites Man page Source code
allSitesName.paraFixSites Man page Source code
allSitesName.parallelSites Man page Source code
as.data.frame.SNPsites Man page Source code
as.data.frame.fixationSites Man page Source code
as.data.frame.parallelSites Man page Source code
as.phylo Man page
as.phylo.fixationIndels Source code
as.phylo.fixationSites Source code
as.phylo.phyMSAmatched Source code
as.phylo.sitePath Source code
as.phylo.sitesMinEntropy Source code
as.treedata Man page
as.treedata.fixationIndels Source code
as.treedata.fixationPath Source code
as.treedata.fixationSites Source code
divergentNode Source code
extractSite Man page Source code
extractSite.fixationSites Man page Source code
extractSite.parallelSites Source code
extractTips Man page Source code
extractTips.fixationSites Man page Source code
extractTips.lineagePath Man page Source code
extractTips.parallelSites Man page Source code
extractTips.sitePara Man page Source code
extractTips.sitePath Man page Source code
fixationIndels Man page Source code
fixationIndels.sitesMinEntropy Man page Source code
fixationPath Man page Source code
fixationPath.fixationSites Man page Source code
fixationPath.sitesMinEntropy Man page Source code
fixationSites Man page Source code
fixationSites.lineagePath Man page Source code
fixationSites.sitesMinEntropy Man page Source code
getReference Source code
getSimilarityMatrix Source code
groupTips Man page Source code
groupTips.fixationPath Man page Source code
groupTips.fixationSites Man page Source code
groupTips.lineagePath Man page Source code
groupTips.phyMSAmatched Man page Source code
groupTips.sitesMinEntropy Man page Source code
h3n2_align Man page
h3n2_align_reduced Man page
h3n2_tree Man page
h3n2_tree_reduced Man page
lineagePath Man page Source code
lineagePath.phyMSAmatched Man page Source code
lineagePath.sneakPeekedPaths Man page Source code
majorSNPtips Source code
mergePaths Source code
minEntropyByComparing Source code
minEntropyByDeleting Source code
minEntropyByInserting Source code
multiFixationSites Man page Source code
multiFixationSites.lineagePath Source code
pairSimilarity Source code
paraFixSites Man page Source code
paraFixSites.lineagePath Man page Source code
paraFixSites.sitesMinEntropy Man page Source code
parallelSites Man page Source code
parallelSites.lineagePath Man page Source code
parallelSites.sitesMinEntropy Man page Source code
phyMSAmatched Man page
plot.fixationIndels Man page Source code
plot.fixationPath Man page Source code
plot.fixationSites Man page Source code
plot.lineagePath Man page Source code
plot.parallelSites Man page Source code
plot.phyMSAmatched Man page Source code
plot.sitePath Man page Source code
plotMutSites Man page Source code
plotMutSites.SNPsites Man page Source code
plotMutSites.fixationSites Man page Source code
plotMutSites.lineagePath Man page Source code
plotMutSites.paraFixSites Man page Source code
plotMutSites.parallelSites Man page Source code
plotSingleSite Man page Source code
plotSingleSite.fixationSites Man page Source code
plotSingleSite.lineagePath Man page Source code
plotSingleSite.parallelSites Man page Source code
plotSingleSite.sitesMinEntropy Source code
print.SNPsites Source code
print.fixationIndels Source code
print.fixationPath Source code
print.fixationSites Source code
print.indelPath Source code
print.lineagePath Source code
print.paraFixSites Source code
print.parallelSites Source code
print.phyMSAmatched Source code
print.sitePara Source code
print.sitePath Source code
print.sitesMinEntropy Source code
read.tree Man page
reexports Man page
sars2_align Man page
sars2_tree Man page
setSiteNumbering Man page Source code
setSiteNumbering.fixationPath Source code
setSiteNumbering.fixationSites Source code
setSiteNumbering.paraFixSites Source code
setSiteNumbering.phyMSAmatched Man page Source code
similarityMatrix Man page Source code
sitePath-deprecated Man page
sitesMinEntropy Man page Source code
sitesMinEntropy.lineagePath Man page Source code
sneakPeek Man page Source code
tableAA Source code
terminalTipsByDist Source code
terminalTipsBySim Source code
zikv_align Man page
zikv_align_reduced Man page
zikv_tree Man page
zikv_tree_reduced Man page
wuaipinglab/sitePath documentation built on July 25, 2021, 9:11 p.m.