Tools for Working With Synteny Objects

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Documentation for package ‘SynExtend’ version 1.12.0

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

Help Pages

as.data.frame.simMat	Similarity Matrices
as.matrix.simMat	Similarity Matrices
as.simMat	Similarity Matrices
as.simMat.matrix	Similarity Matrices
as.simMat.vector	Similarity Matrices
Behdenna.ProtWeaver	Presence/Absence Predictions for ProtWeaver
BlastSeqs	Run BLAST queries from R
BlockExpansion	Attempt to expand blocks of paired features in a 'PairSummaries' object.
BlockReconciliation	Rejection scheme for asyntenic predicted pairs
BuiltInEnsembles	Pretrained ProtWeaver Ensemble Models
CIDist	Clustering Information Distance
CIDist_NullDist	Simulated Null Distributions for CI Distance
Coloc.ProtWeaver	Co-localization Predictions for ProtWeaver
ContextTree.ProtWeaver	Distance Matrix Predictions for ProtWeaver
CorrGL.ProtWeaver	Presence/Absence Predictions for ProtWeaver
dendrapply	Apply a Function to All Nodes of a Dendrogram
Diag	Similarity Matrices
Diag.simMat	Similarity Matrices
Diag<-	Similarity Matrices
Diag<-.simMat	Similarity Matrices
DisjointSet	Return single linkage clusters from 'PairSummaries' objects.
DPhyloStatistic	D-Statistic for Binary States on a Phylogeny
Endosymbionts_GeneCalls	Example genecalls
Endosymbionts_LinkedFeatures	Example synteny links
Endosymbionts_Pairs01	Example predicted pairs
Endosymbionts_Pairs02	Example predicted pairs
Endosymbionts_Pairs03	Example predicted pairs
Endosymbionts_Sets	A list of disjoint sets.
Endosymbionts_Synteny	A synteny object
EstimateRearrangementScenarios	Estimate Genome Rearrangement Events with Double Cut and Join Operations
EstimRearrScen	Estimate Genome Rearrangement Events with Double Cut and Join Operations
ExampleStreptomycesData	Example ProtWeaver Input Data from _Streptomyces_ Species
ExtractBy	Extract and organize 'DNAStringSets's.
FindSets	Find all single linkage clusters in an undirected pairs list.
GainLoss.ProtWeaver	Presence/Absence Predictions for ProtWeaver
Generic	Model for predicting PID based on k-mer statistics
gffToDataFrame	Generate a DataFrame of gene calls from a gff3 file
Hamming.ProtWeaver	Presence/Absence Predictions for ProtWeaver
Jaccard.ProtWeaver	Presence/Absence Predictions for ProtWeaver
JRFDist	Jaccard-Robinson-Foulds Distance
KFDist	Kuhner-Felsenstein Distance
LinkedPairs-class	Tables of where syntenic hits link pairs of genes
MirrorTree.ProtWeaver	Distance Matrix Predictions for ProtWeaver
MoransI	Moran's _I_ Spatial Autocorrelation Index
MutualInformation.ProtWeaver	Presence/Absence Predictions for ProtWeaver
NucleotideOverlap	Tabulating Pairs of Genomic Sequences
PairSummaries	Summarize connected pairs in a LinkedPairs object
PhyloDistance	Calculate Distance between Unrooted Phylogenies
PhyloDistance-CI	Clustering Information Distance
PhyloDistance-JRF	Jaccard-Robinson-Foulds Distance
PhyloDistance-KF	Kuhner-Felsenstein Distance
PhyloDistance-RF	Robinson-Foulds Distance
plot.ProtWeb	Plot predictions in a ProtWeb object
predict.ProtWeaver	Make predictions with ProtWeaver objects
print.LinkedPairs	Tables of where syntenic hits link pairs of genes
print.simMat	Similarity Matrices
ProfDCA.ProtWeaver	Presence/Absence Predictions for ProtWeaver
ProtWeaver	ProtWeaver: Predicting Protein Functional Association Networks
ProtWeaver-class	ProtWeaver: Predicting Protein Functional Association Networks
ProtWeaver-ColocPreds	Co-localization Predictions for ProtWeaver
ProtWeaver-DMPreds	Distance Matrix Predictions for ProtWeaver
ProtWeaver-PAPreds	Presence/Absence Predictions for ProtWeaver
ProtWeaver-ResiduePreds	Residue Level Predictions for ProtWeaver
ProtWeaver-utils	ProtWeaver: Predicting Protein Functional Association Networks
ProtWeb	ProtWeb: Predictions from ProtWeaver
ResidueMI.ProtWeaver	Residue Level Predictions for ProtWeaver
RFDist	Robinson-Foulds Distance
SelectByK	Predicted pair trimming using K-means.
SequenceSimilarity	Return a numeric value that represents the similarity between two aligned sequences as determined by a provided subsitution matrix.
simMat	Similarity Matrices
simMat-class	Similarity Matrices
SpeciesTree	ProtWeaver: Predicting Protein Functional Association Networks
SpeciesTree.ProtWeaver	ProtWeaver: Predicting Protein Functional Association Networks
SubSetPairs	Subset a "PairSummaries" object.
SuperTree	Create a Species Tree from Gene Trees
SuperTreeEx	Example Dendrograms
[.LinkedPairs	Tables of where syntenic hits link pairs of genes