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A C D G H K L M N O P R S T V misc
| FindMyFriends-package | FindMyFriends: Comparative microbial genomics in R |
| addGenomes | Add new organisms to an existing pangenome |
| addGenomes-method | Add new organisms to an existing pangenome |
| addGroupInfo | Safely add group info |
| addGroupInfo-method | Safely add group info |
| addOrgInfo | Safely add organisms info |
| addOrgInfo-method | Safely add organisms info |
| as | Base class for pangenomic data |
| cdhitGrouping | Gene grouping by preclustering with CD-HIT |
| cdhitGrouping-method | Gene grouping by preclustering with CD-HIT |
| collapseParalogues | Merge paralogue gene groups into new gene groups |
| collapseParalogues-method | Merge paralogue gene groups into new gene groups |
| defaults | Access default values for a pgVirtual subclass object |
| defaults-method | Access default values for a pgVirtual subclass object |
| defaults<- | Access default values for a pgVirtual subclass object |
| defaults<--method | Access default values for a pgVirtual subclass object |
| geneLocation | Get gene location for all genes |
| geneLocation-method | Get gene location for all genes |
| geneNames | Get and set the names of the genes in the pangenome |
| geneNames-method | Get and set the names of the genes in the pangenome |
| geneNames<- | Get and set the names of the genes in the pangenome |
| geneNames<--method | Get and set the names of the genes in the pangenome |
| genes | Extract gene sequences from a pangenome |
| genes-method | Extract gene sequences from a pangenome |
| geneWidth | Get the sequence length of each gene |
| geneWidth-method | Get the sequence length of each gene |
| getNeighborhood | Extract a graph representation of a gene group neighborhood |
| getNeighborhood-method | Extract a graph representation of a gene group neighborhood |
| getRep | Get a representative sequence for each gene group |
| getRep-method | Get a representative sequence for each gene group |
| gpcGrouping | Guided Pairwise Comparison grouping of genes |
| gpcGrouping-method | Guided Pairwise Comparison grouping of genes |
| graphGrouping | Use igraph to create gene grouping from a similarity matrix |
| graphGrouping-method | Use igraph to create gene grouping from a similarity matrix |
| groupInfo | Get and set information about gene group |
| groupInfo-method | Get and set information about gene group |
| groupInfo<- | Get and set information about gene group |
| groupInfo<--method | Get and set information about gene group |
| groupNames | Get and set the names of gene groups in the pangenome |
| groupNames-method | Get and set the names of gene groups in the pangenome |
| groupNames<- | Get and set the names of gene groups in the pangenome |
| groupNames<--method | Get and set the names of gene groups in the pangenome |
| groupStat | Calculate statistics about each gene group |
| groupStat-method | Calculate statistics about each gene group |
| hasGeneGroups | Check whether gene groups are defined |
| hasGeneGroups-method | Check whether gene groups are defined |
| hasGeneInfo | Checks for existance of gene location information |
| hasGeneInfo-method | Checks for existance of gene location information |
| hasParalogueLinks | Checks whether linking of paralogues has been done |
| hasParalogueLinks-method | Checks whether linking of paralogues has been done |
| kmerLink | Link gene groups by homology |
| kmerLink-method | Link gene groups by homology |
| kmerSimilarity | Calculate a similarity matrix based on kmers |
| kmerSimilarity-method | Calculate a similarity matrix based on kmers |
| kmerSplit | Split gene groups based on similarity |
| kmerSplit-method | Split gene groups based on similarity |
| length-method | Base class for pangenomic data |
| manualGrouping | Define gene grouping manually |
| manualGrouping-method | Define gene grouping manually |
| neighborhoodSplit | Split gene groups by neighborhood synteny |
| neighborhoodSplit-method | Split gene groups by neighborhood synteny |
| nGeneGroups | Get the number of gene groups in a pangenome |
| nGeneGroups-method | Get the number of gene groups in a pangenome |
| nGenes | Get the total number of genes in a pangenome |
| nGenes-method | Get the total number of genes in a pangenome |
| nOrganisms | Get the number of organisms represented in a pangenome |
| nOrganisms-method | Get the number of organisms represented in a pangenome |
| orgInfo | Get and set information about organisms |
| orgInfo-method | Get and set information about organisms |
| orgInfo<- | Get and set information about organisms |
| orgInfo<--method | Get and set information about organisms |
| orgNames | Get and set the names of organisms in the pangenome |
| orgNames-method | Get and set the names of organisms in the pangenome |
| orgNames<- | Get and set the names of organisms in the pangenome |
| orgNames<--method | Get and set the names of organisms in the pangenome |
| orgStat | Calculate statistics about each organism |
| orgStat-method | Calculate statistics about each organism |
| pangenome | Construct a pangenome from fasta files |
| pcGraph | Calculate the panchromosome graph |
| pcGraph-method | 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 |
| pgMatrix-method | 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 |
| plotEvolution-method | Plot the evolution in gene groups |
| plotGroup | Plot the similarities of genes within a group |
| plotGroup-method | Plot the similarities of genes within a group |
| plotNeighborhood | Plot the neighborhood of a gene group |
| plotNeighborhood-method | Plot the neighborhood of a gene group |
| plotSimilarity | Create a heatplot with similarities between all organisms |
| plotSimilarity-method | Create a heatplot with similarities between all organisms |
| plotStat | Plot (very) basic statistics on the pangenome |
| plotStat-method | Plot (very) basic statistics on the pangenome |
| plotTree | Plot a dendrogram of the organisms in a pangenome |
| plotTree-method | Plot a dendrogram of the organisms in a pangenome |
| readAnnot | Import annotation from an .annot file |
| removeGene | Remove genes from a pangenome |
| removeGene-method | Remove genes from a pangenome |
| reportGroupChanges | Reports the change in grouping |
| seqToGeneGroup | Get gene-to-genegroup relationship |
| seqToGeneGroup-method | Get gene-to-genegroup relationship |
| seqToOrg | Get gene-to-organism relationship |
| seqToOrg-method | Get gene-to-organism relationship |
| show-method | Base class for pangenomic data |
| translated | Check the sequence type of the pangenome |
| translated-method | Check the sequence type of the pangenome |
| variableRegions | Detect regions of high variability in the panchromosome |
| variableRegions-method | Detect regions of high variability in the panchromosome |
| .fillDefaults | Assign object defaults to missing values |
| .loadPgExample | Load an example pangenome |
| [-method | Base class for pangenomic data |
| [[-method | Base class for pangenomic data |