FindMyFriends: Microbial Comparative Genomics in R

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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.

Author
Thomas Lin Pedersen
Date of publication
None
Maintainer
Thomas Lin Pedersen <thomasp85@gmail.com>
License
GPL (>=2)
Version
1.4.0
URLs

View on Bioconductor

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

Files in this package

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