FindMyFriends: Microbial Comparative Genomics in R
Version 1.6.0

A framework for doing microbial comparative genomics in R. The main purpose of the package is assisting in the creation of pangenome matrices where genes from related organisms are grouped by similarity, as well as the analysis of these data. FindMyFriends provides many novel approaches to doing pangenome analysis and supports a gene grouping algorithm that scales linearly, thus making the creation of huge pangenomes feasible.

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AuthorThomas Lin Pedersen
Bioconductor views Clustering ComparativeGenomics DataRepresentation GenomicVariation GraphAndNetwork SequenceMatching
Date of publicationNone
MaintainerThomas Lin Pedersen <thomasp85@gmail.com>
LicenseGPL (>=2)
Version1.6.0
URL https://github.com/thomasp85/FindMyFriends
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("FindMyFriends")

Man pages

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
fillDefaults: Assign object defaults to missing values
FindMyFriends-package: FindMyFriends: Comparative microbial genomics in R
geneLocation: Get gene location for all genes
geneNames: Get and set the names of the genes in the pangenome
genes: Extract gene sequences from a pangenome
geneWidth: Get the sequence length of each gene
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
internalGroupGenes: Add gene grouping to pangenome
internalMergePangenomes: Merge information from two pangenomes
internalMetadata: Add metadata to the pangenome
kmerLink: Link gene groups by homology
kmerSimilarity: Calculate a similarity matrix based on kmers
kmerSplit: Split gene groups based on similarity
loadPgExample: Load an example pangenome
manualGrouping: Define gene grouping manually
neighborhoodSplit: Split gene groups by neighborhood synteny
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
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...
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

Functions

.fillDefaults Man page
.loadPgExample Man page
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
collectNeighbors Source code
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
fillDefaults 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
getRoute Source code
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
loadPgExample Source code
locateCycles Source code
makeProgress Source code
manualGrouping Man page
manualGrouping,pgVirtual,integer-method Man page
manualGrouping,pgVirtual,list-method Man page
matchGroups Source code
mergeCycles 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
orgGraphs 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
scaleRange 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
summarizeCycles Source code
trailGroups Source code
trailsToGraph 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

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/FindMyFriends-package.R
R/RcppExports.R
R/aaa.R
R/constructor.R
R/generics.R
R/ggGraph.R
R/grouping.R
R/investigating.R
R/linearKernel.R
R/linking.R
R/modifying.R
R/pgFull.R
R/pgFullLoc.R
R/pgInMem.R
R/pgInMemLoc.R
R/pgLM.R
R/pgLMLoc.R
R/pgSlim.R
R/pgSlimLoc.R
R/pgVirtual.R
R/pgVirtualLoc.R
R/progress.R
R/similarities.R
R/splitting.R
README.md
build
build/vignette.rds
inst
inst/doc
inst/doc/FindMyFriends_intro.R
inst/doc/FindMyFriends_intro.Rmd
inst/doc/FindMyFriends_intro.html
inst/extdata
inst/extdata/Mycoplasma.zip
inst/extdata/examplePG
inst/extdata/examplePG/example.annot
inst/extdata/examplePG/groupsNS.txt
inst/extdata/examplePG/groupsWG.txt
inst/extdata/examplePG/paraNS.txt
inst/extdata/examplePG/paraWG.txt
man
man/FindMyFriends-package.Rd
man/addGenomes.Rd
man/addGroupInfo.Rd
man/addOrgInfo.Rd
man/cdhitGrouping.Rd
man/collapseParalogues.Rd
man/defaults.Rd
man/fillDefaults.Rd
man/geneLocation.Rd
man/geneNames.Rd
man/geneWidth.Rd
man/genes.Rd
man/getNeighborhood.Rd
man/getRep.Rd
man/gpcGrouping.Rd
man/graphGrouping.Rd
man/groupInfo.Rd
man/groupNames.Rd
man/groupStat.Rd
man/hasGeneGroups.Rd
man/hasGeneInfo.Rd
man/hasParalogueLinks.Rd
man/internalGroupGenes.Rd
man/internalMergePangenomes.Rd
man/internalMetadata.Rd
man/kmerLink.Rd
man/kmerSimilarity.Rd
man/kmerSplit.Rd
man/loadPgExample.Rd
man/manualGrouping.Rd
man/nGeneGroups.Rd
man/nGenes.Rd
man/nOrganisms.Rd
man/neighborhoodSplit.Rd
man/orgInfo.Rd
man/orgNames.Rd
man/orgStat.Rd
man/pangenome.Rd
man/pcGraph.Rd
man/pgFull-class.Rd
man/pgFullLoc-class.Rd
man/pgInMem-class.Rd
man/pgInMemLoc-class.Rd
man/pgLM-class.Rd
man/pgLMLoc-class.Rd
man/pgMatrix.Rd
man/pgSlim-class.Rd
man/pgSlimLoc-class.Rd
man/pgVirtual-class.Rd
man/pgVirtualLoc-class.Rd
man/plotEvolution.Rd
man/plotGroup.Rd
man/plotNeighborhood.Rd
man/plotSimilarity.Rd
man/plotStat.Rd
man/plotTree.Rd
man/readAnnot.Rd
man/removeGene.Rd
man/reportGroupChanges.Rd
man/seqToGeneGroup.Rd
man/seqToOrg.Rd
man/translated.Rd
man/variableRegions.Rd
src
src/RcppExports.cpp
src/cdhit-bombs.cpp
src/cdhit-common.cpp
src/cdhit-common.h
src/cdhit-est.cpp
src/cdhit.cpp
src/fastaFunctions.cpp
src/fmf-common.cpp
src/fmf-common.h
src/linearKernel.cpp
src/neighborhoodSim.cpp
src/panSim.cpp
src/progress.cpp
src/progress.h
src/smallgraph.cpp
src/smallgraph.h
tests
tests/testthat
tests/testthat.R
tests/testthat/test-GPC.R
tests/testthat/test-addGenomes.R
tests/testthat/test-constructor.R
tests/testthat/test-defaults.R
tests/testthat/test-geneLocation.R
tests/testthat/test-grouping.R
tests/testthat/test-investigating.R
tests/testthat/test-linking.R
tests/testthat/test-loadPgExample.R
tests/testthat/test-modifying.R
tests/testthat/test-orgCompare.R
tests/testthat/test-parallelLinearKernel.R
tests/testthat/test-pgFull.R
tests/testthat/test-pgLM.R
tests/testthat/test-pgSlim.R
tests/testthat/test-similarities.R
tests/testthat/test-splitAndBind.R
tests/testthat/test-splitting.R
vignettes
vignettes/FindMyFriends_intro.Rmd
vignettes/styles.css
FindMyFriends documentation built on May 20, 2017, 11:03 p.m.