.fillDefaults           Assign object defaults to missing values
.loadPgExample          Load an example pangenome
FindMyFriends-package   FindMyFriends: Comparative microbial genomics
                        in R
addGenomes              Add new organisms to an existing pangenome
addGroupInfo            Safely add group info
addOrgInfo              Safely add organisms info
cdhitGrouping           Gene grouping by preclustering with CD-HIT
collapseParalogues      Merge paralogue gene groups into new gene
                        groups
defaults                Access default values for a pgVirtual subclass
                        object
geneLocation            Get gene location for all genes
geneNames               Get and set the names of the genes in the
                        pangenome
geneWidth               Get the sequence length of each gene
genes                   Extract gene sequences from a pangenome
getNeighborhood         Extract a graph representation of a gene group
                        neighborhood
getRep                  Get a representative sequence for each gene
                        group
gpcGrouping             Guided Pairwise Comparison grouping of genes
graphGrouping           Use igraph to create gene grouping from a
                        similarity matrix
groupInfo               Get and set information about gene group
groupNames              Get and set the names of gene groups in the
                        pangenome
groupStat               Calculate statistics about each gene group
hasGeneGroups           Check whether gene groups are defined
hasGeneInfo             Checks for existance of gene location
                        information
hasParalogueLinks       Checks whether linking of paralogues has been
                        done
kmerLink                Link gene groups by homology
kmerSimilarity          Calculate a similarity matrix based on kmers
kmerSplit               Split gene groups based on similarity
manualGrouping          Define gene grouping manually
nGeneGroups             Get the number of gene groups in a pangenome
nGenes                  Get the total number of genes in a pangenome
nOrganisms              Get the number of organisms represented in a
                        pangenome
neighborhoodSplit       Split gene groups by neighborhood synteny
orgInfo                 Get and set information about organisms
orgNames                Get and set the names of organisms in the
                        pangenome
orgStat                 Calculate statistics about each organism
pangenome               Construct a pangenome from fasta files
pcGraph                 Calculate the panchromosome graph
pgFull-class            Class for in memory pangenome data
pgFullLoc-class         Class for in memory pangenome data with
                        location information
pgInMem-class           FindMyFriends standard base class for
                        pangenomic data
pgInMemLoc-class        Superclass for gene location aware pangenome
pgLM-class              Class for reference based pangenome data
pgLMLoc-class           Class for reference based pangenome data with
                        location information
pgMatrix                Get the pangenome matrix
pgSlim-class            Class for pangenome data with no reference to
                        genes
pgSlimLoc-class         Class for pangenome data with no reference to
                        genes
pgVirtual-class         Base class for pangenomic data
pgVirtualLoc-class      Superclass for gene location aware pangenome
plotEvolution           Plot the evolution in gene groups
plotGroup               Plot the similarities of genes within a group
plotNeighborhood        Plot the neighborhood of a gene group
plotSimilarity          Create a heatplot with similarities between all
                        organisms
plotStat                Plot (very) basic statistics on the pangenome
plotTree                Plot a dendrogram of the organisms in a
                        pangenome
readAnnot               Import annotation from an .annot file
removeGene              Remove genes from a pangenome
reportGroupChanges      Reports the change in grouping
seqToGeneGroup          Get gene-to-genegroup relationship
seqToOrg                Get gene-to-organism relationship
translated              Check the sequence type of the pangenome
variableRegions         Detect regions of high variability in the
                        panchromosome
