# Microbial Comparative Genomics in R

## Documentation for package ‘FindMyFriends’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D G H K L M N O P R S T V misc

FindMyFriends-package | FindMyFriends: Comparative microbial genomics in R

## -- A --

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

## -- C --

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

## -- D --

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

## -- G --

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

## -- H --

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

## -- K --

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

## -- L --

length-method | Base class for pangenomic data

## -- M --

manualGrouping | Define gene grouping manually
manualGrouping-method | Define gene grouping manually

## -- N --

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

## -- O --

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

## -- P --

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

## -- R --

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

## -- S --

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

## -- T --

translated | Check the sequence type of the pangenome
translated-method | Check the sequence type of the pangenome

## -- V --

variableRegions | Detect regions of high variability in the panchromosome
variableRegions-method | Detect regions of high variability in the panchromosome

## -- misc --

.fillDefaults | Assign object defaults to missing values
.loadPgExample | Load an example pangenome
[-method | Base class for pangenomic data
[[-method | Base class for pangenomic data