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