Man pages for FindMyFriends
Microbial Comparative Genomics in R

addGenomesAdd new organisms to an existing pangenome
addGroupInfoSafely add group info
addOrgInfoSafely add organisms info
cdhitGroupingGene grouping by preclustering with CD-HIT
collapseParaloguesMerge paralogue gene groups into new gene groups
defaultsAccess default values for a pgVirtual subclass object
fillDefaultsAssign object defaults to missing values
FindMyFriends-packageFindMyFriends: Comparative microbial genomics in R
geneLocationGet gene location for all genes
geneNamesGet and set the names of the genes in the pangenome
genesExtract gene sequences from a pangenome
geneWidthGet the sequence length of each gene
getNeighborhoodExtract a graph representation of a gene group neighborhood
getRepGet a representative sequence for each gene group
gpcGroupingGuided Pairwise Comparison grouping of genes
graphGroupingUse igraph to create gene grouping from a similarity matrix
groupInfoGet and set information about gene group
groupNamesGet and set the names of gene groups in the pangenome
groupStatCalculate statistics about each gene group
hasGeneGroupsCheck whether gene groups are defined
hasGeneInfoChecks for existance of gene location information
hasParalogueLinksChecks whether linking of paralogues has been done
internalGroupGenesAdd gene grouping to pangenome
internalMergePangenomesMerge information from two pangenomes
internalMetadataAdd metadata to the pangenome
kmerLinkLink gene groups by homology
kmerSimilarityCalculate a similarity matrix based on kmers
kmerSplitSplit gene groups based on similarity
loadPgExampleLoad an example pangenome
manualGroupingDefine gene grouping manually
neighborhoodSplitSplit gene groups by neighborhood synteny
nGeneGroupsGet the number of gene groups in a pangenome
nGenesGet the total number of genes in a pangenome
nOrganismsGet the number of organisms represented in a pangenome
orgInfoGet and set information about organisms
orgNamesGet and set the names of organisms in the pangenome
orgStatCalculate statistics about each organism
pangenomeConstruct a pangenome from fasta files
pcGraphCalculate the panchromosome graph
pgFull-classClass for in memory pangenome data
pgFullLoc-classClass for in memory pangenome data with location information
pgInMem-classFindMyFriends standard base class for pangenomic data
pgInMemLoc-classSuperclass for gene location aware pangenome
pgLM-classClass for reference based pangenome data
pgLMLoc-classClass for reference based pangenome data with location...
pgMatrixGet the pangenome matrix
pgSlim-classClass for pangenome data with no reference to genes
pgSlimLoc-classClass for pangenome data with no reference to genes
pgVirtual-classBase class for pangenomic data
pgVirtualLoc-classSuperclass for gene location aware pangenome
plotEvolutionPlot the evolution in gene groups
plotGroupPlot the similarities of genes within a group
plotNeighborhoodPlot the neighborhood of a gene group
plotSimilarityCreate a heatplot with similarities between all organisms
plotStatPlot (very) basic statistics on the pangenome
plotTreePlot a dendrogram of the organisms in a pangenome
readAnnotImport annotation from an .annot file
removeGeneRemove genes from a pangenome
reportGroupChangesReports the change in grouping
seqToGeneGroupGet gene-to-genegroup relationship
seqToOrgGet gene-to-organism relationship
translatedCheck the sequence type of the pangenome
variableRegionsDetect regions of high variability in the panchromosome
FindMyFriends documentation built on May 31, 2017, 3:49 p.m.