API for FindMyFriends
Microbial Comparative Genomics in R

Global functions
.fillDefaults Man page Source code
.loadPgExample Man page Source code
FindMyFriends-package Man page
[,pgVirtual,character,ANY,ANY-method Man page
[,pgVirtual,integer,ANY,ANY-method Man page
[,pgVirtual,logical,ANY,ANY-method Man page
[,pgVirtual,numeric,ANY,ANY-method Man page
[[,pgVirtual,ANY,ANY-method Man page
addGenomes Man page
addGenomes,pgVirtual,pgVirtual-method Man page
addGroupInfo Man page
addGroupInfo,pgVirtual-method Man page
addOrgInfo Man page
addOrgInfo,pgVirtual-method Man page
anyParalogues Source code
as Man page
calcGroupInfo Source code
cdhit Source code
cdhitC Source code
cdhitGrouping Man page
cdhitGrouping,pgVirtual-method Man page
cdhitestC Source code
clustersFromAdjMatrix Source code
collapseParalogues Man page
collapseParalogues,pgVirtual-method Man page
convertGrouping Source code
createBar Source code
createPanMatrix Source code
createProgress Source code
cutK Source code
defaults Man page
defaults,pgVirtual-method Man page
defaults<- Man page
defaults<-,pgVirtual-method Man page
evolBoot Source code
evolMan Source code
extractCliques Source code
fillTree Source code
findIn Source code
formatSeconds Source code
geneLocation Man page
geneLocation,pgInMemLoc-method Man page
geneNames Man page
geneNames,pgFull-method Man page
geneNames,pgLM-method Man page
geneNames,pgSlim-method Man page
geneNames<- Man page
geneNames<-,pgFull-method Man page
geneNames<-,pgLM-method Man page
geneNames<-,pgSlim-method Man page
geneWidth Man page
geneWidth,pgFull-method Man page
geneWidth,pgLM-method Man page
geneWidth,pgSlim-method Man page
genes Man page
genes,pgFull,character-method Man page
genes,pgFull,missing-method Man page
genes,pgLM,character-method Man page
genes,pgLM,missing-method Man page
genes,pgSlim,character-method Man page
genes,pgSlim,missing-method Man page
getChunks Source code
getCliques Source code
getClusters Source code
getNeighborhood Man page
getNeighborhood,pgVirtualLoc-method Man page
getNeighbors Source code
getPgMatrix Source code
getPotentials Source code
getRep Man page
getRep,pgVirtual,character-method Man page
getSeqInfo Source code
gpcGrouping Man page
gpcGrouping,pgVirtual-method Man page
graphGrouping Man page
graphGrouping,pgVirtual-method Man page
groupDistribution Source code
groupGenes Man page
groupGenes,pgInMem-method Man page
groupGenes,pgVirtual-method Man page
groupHasParalogues Source code
groupInfo Man page
groupInfo,pgInMem-method Man page
groupInfo<- Man page
groupInfo<-,pgInMem-method Man page
groupNames Man page
groupNames,pgInMem-method Man page
groupNames<- Man page
groupNames<-,pgInMem-method Man page
groupNeighbors Source code
groupStat Man page
groupStat,pgVirtual-method Man page
groupToGraph Source code
hasGeneGroups Man page
hasGeneGroups,pgVirtual-method Man page
hasGeneInfo Man page
hasGeneInfo,pgVirtual-method Man page
hasParalogueLinks Man page
hasParalogueLinks,pgVirtual-method Man page
igGroup Source code
igMembers Source code
internal-groupGenes Man page
internal-mergePangenomes Man page
internal-metadata Man page
kmerDist Source code
kmerLink Man page
kmerLink,pgVirtual-method Man page
kmerSim Source code
kmerSimilarity Man page
kmerSimilarity,pgVirtual-method Man page
kmerSplit Man page
kmerSplit,pgVirtual-method Man page
kmerSplitting Source code
largestInfo Source code
length,pgVirtual-method Man page
lkFMF Source code
lkFMFmat Source code
lkMatrix Source code
lkMembers Source code
lkParallel Source code
lkParallelLM Source code
makeProgress Source code
manualGrouping Man page
manualGrouping,pgVirtual,integer-method Man page
manualGrouping,pgVirtual,list-method Man page
matchGroups Source code
mergeGroups Source code
mergeGroupsByNeighbors Source code
mergeInfo Source code
mergePangenomes Man page
mergePangenomes,pgFull,pgFull-method Man page
mergePangenomes,pgFullLoc,pgFullLoc-method Man page
mergePangenomes,pgInMem,pgInMem-method Man page
mergePangenomes,pgLM,pgLM-method Man page
mergePangenomes,pgLMLoc,pgLMLoc-method Man page
mergePangenomes,pgSlimLoc,pgSlimLoc-method Man page
mergeSims Source code
nGeneGroups Man page
nGeneGroups,pgVirtual-method Man page
nGenes Man page
nGenes,pgVirtual-method Man page
nOrganisms Man page
nOrganisms,pgVirtual-method Man page
nSeqs Source code
neighborSplitting Source code
neighborhoodMerge Source code
neighborhoodSim Source code
neighborhoodSplit Man page
neighborhoodSplit,pgVirtualLoc-method Man page
orgExRep Source code
orgInfo Man page
orgInfo,pgInMem-method Man page
orgInfo<- Man page
orgInfo<-,pgInMem-method Man page
orgNames Man page
orgNames,pgInMem-method Man page
orgNames<- Man page
orgNames<-,pgInMem-method Man page
orgStat Man page
orgStat,pgVirtual-method Man page
orgTree Source code
pairToIndex Source code
panGroups Source code
panSim Source code
pangenome Man page Source code
paralogueInd Source code
pcGraph Man page
pcGraph,pgVirtualLoc-method Man page
pgDist Source code
pgFull-class Man page
pgFullLoc-class Man page
pgInMem-class Man page
pgInMemLoc-class Man page
pgLM-class Man page
pgLMLoc-class Man page
pgMatrix Man page
pgMatrix,pgVirtual-method Man page
pgSim Source code
pgSlim-class Man page
pgSlimLoc-class Man page
pgVirtual-class Man page
pgVirtualLoc-class Man page
plotEvolution Man page
plotEvolution,pgVirtual-method Man page
plotGroup Man page
plotGroup,pgVirtual-method Man page
plotNeighborhood Man page
plotNeighborhood,pgVirtualLoc-method Man page
plotSimilarity Man page
plotSimilarity,pgVirtual-method Man page
plotStat Man page
plotStat,pgVirtual-method Man page
plotTree Man page
plotTree,pgVirtual-method Man page
prodigalParse Source code
progress Source code
rbindGtable Source code
rbindMat Source code
rbind_gtable Source code
readAnnot Man page Source code
recurseCompPar Source code
recurseCompare Source code
removeGene Man page
removeGene,pgInMem,missing,missing,missing,numeric-method Man page
removeGene,pgVirtual,character,character,missing,missing-method Man page
removeGene,pgVirtual,character,missing,missing,missing-method Man page
removeGene,pgVirtual,character,numeric,missing,missing-method Man page
removeGene,pgVirtual,missing,character,missing,missing-method Man page
removeGene,pgVirtual,missing,character,missing,numeric-method Man page
removeGene,pgVirtual,missing,missing,character,missing-method Man page
removeGene,pgVirtual,missing,missing,character,numeric-method Man page
removeGene,pgVirtual,missing,missing,numeric,missing-method Man page
removeGene,pgVirtual,missing,missing,numeric,numeric-method Man page
removeGene,pgVirtual,missing,numeric,missing,missing-method Man page
removeGene,pgVirtual,missing,numeric,missing,numeric-method Man page
removeIndex Source code
reportGroupChanges Man page Source code
resizeDataFrame Source code
safeAAread Source code
safeDNAread Source code
seqToGeneGroup Man page
seqToGeneGroup,pgInMem-method Man page
seqToOrg Man page
seqToOrg,pgInMem-method Man page
setGroupInfo Man page
setGroupInfo,pgInMem-method Man page
setOrgInfo Man page
setOrgInfo,pgInMem-method Man page
show,pgVirtual-method Man page
splitStringSet Source code
trailGroups Source code
transformSim Source code
translated Man page
translated,pgVirtual-method Man page
variableRegions Man page
variableRegions,pgVirtualLoc-method Man page
weaveChunks Source code
widthSim Source code
FindMyFriends documentation built on April 29, 2020, 5:05 a.m.