Tools for Working With Synteny Objects

Documentation for package ‘SynExtend’ version 1.21.1

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A B C D E F G H J K L M N O P R S T W misc

-- A --

AAHitScoping	Adjust the scope of kmer hits between feature and genome space.
Ancestral.EvoWeaver	Sequence Level Predictions for EvoWeaver
ApproximateBackground	Return the approximate background alignment score for a series of paired sequences.
as.data.frame.simMat	Similarity Matrices
as.dendrogram.DecisionTree	Decision Trees for Random Forests
as.matrix.simMat	Similarity Matrices
as.simMat	Similarity Matrices
as.simMat.matrix	Similarity Matrices
as.simMat.vector	Similarity Matrices

-- B --

Behdenna.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
BlastSeqs	Run BLAST queries from R
BlockByRank	Return simple summaries of blocks of candidate pairs.
BlockExpansion	Attempt to expand blocks of paired features in a 'PairSummaries' object.
BlockReconciliation	Rejection scheme for asyntenic predicted pairs
BuiltInEnsembles	Pretrained EvoWeaver Ensemble Models

-- C --

CheckAgainstReport	Pull an assembly from the NCBI FTP site.
CIDist	Clustering Information Distance
CIDist_NullDist	Simulated Null Distributions for CI Distance
ClusterByK	Predicted pair trimming using K-means.
CompetePairs	Find the best match pair in cases where ambiguity exists.
CorrGL.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver

-- D --

DecisionTree-class	Decision Trees for Random Forests
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

-- E --

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
EstimateExoLabel	Estimate ExoLabel Disk Consumption
EstimateRearrangementScenarios	Estimate Genome Rearrangement Scenarios with Double Cut and Join Operations
EstimRearrScen	Estimate Genome Rearrangement Scenarios with Double Cut and Join Operations
EvoWeaver	EvoWeaver: Identifying Gene Functional Associations from Coevolutionary Signals
EvoWeaver-class	EvoWeaver: Identifying Gene Functional Associations from Coevolutionary Signals
EvoWeaver-GOPreds	Gene Organization Predictions for EvoWeaver
EvoWeaver-PPPreds	Phylogenetic Profiling Predictions for EvoWeaver
EvoWeaver-PSPreds	Phylogenetic Structure Predictions for EvoWeaver
EvoWeaver-SLPreds	Sequence Level Predictions for EvoWeaver
EvoWeaver-utils	EvoWeaver: Identifying Gene Functional Associations from Coevolutionary Signals
EvoWeb	EvoWeb: Predictions from EvoWeaver
ExampleStreptomycesData	Example EvoWeaver Input Data from _Streptomyces_ Species
ExoLabel	ExoLabel: Out-of-Memory Fast Label Propagation
ExpandDiagonal	Attempt to expand blocks of paired features in a 'PairSummaries' object.
ExtantJaccard.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
ExtractBy	Extract and organize 'DNAStringSets's.

-- F --

FastQFromSRR	Get Sequencing Data from the SRA
FindSets	Find all single linkage clusters in an undirected pairs list.
FitchParsimony	Calculate ancestral states using Fitch Parsimony

-- G --

GeneDistance.EvoWeaver	Gene Organization Predictions for EvoWeaver
Generic	Model for predicting PID based on k-mer statistics
GeneVector.EvoWeaver	Sequence Level Predictions for EvoWeaver
gffToDataFrame	Generate a DataFrame of gene calls from a gff3 file
GLDistance.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
GLMI.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver

-- H --

Hamming.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
HitConsensus	Return a numeric measure of whether kmer hits linking two genomic features are in linearly similar locations in both features.

-- J --

JRFDist

Jaccard-Robinson-Foulds Distance and Nye Similarity

-- K --

KFDist

Kuhner-Felsenstein Distance

-- L --

LinkedPairs-class

Tables of where syntenic hits link pairs of genes

-- M --

MakeBlastDb	Create a BLAST Database from R
MoranI	Moran's _I_ Spatial Autocorrelation Index
MoransI.EvoWeaver	Gene Organization Predictions for EvoWeaver

-- N --

NormVec	Unit normalize a vector
NucleotideOverlap	Tabulating Pairs of Genomic Sequences

-- O --

OneSite	Calculate a site on a right hyperbola.
OrientationMI.EvoWeaver	Gene Organization Predictions for EvoWeaver

-- P --

PairSummaries	Summarize connected pairs in a LinkedPairs object
PAJaccard.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
PAOverlap.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver
PhyloDistance	Calculate Distance between Unrooted Phylogenies
PhyloDistance-CI	Clustering Information Distance
PhyloDistance-JRF	Jaccard-Robinson-Foulds Distance and Nye Similarity
PhyloDistance-KF	Kuhner-Felsenstein Distance
PhyloDistance-RF	Robinson-Foulds Distance
plot.DecisionTree	Decision Trees for Random Forests
plot.EvoWeb	Plot predictions in a EvoWeb object
predict.EvoWeaver	Make predictions with EvoWeaver objects
predict.RandForest	Classification and Regression with Random Forests
PrepareSeqs	Add feature sequences to Decipher databases.
print.LinkedPairs	Tables of where syntenic hits link pairs of genes
print.simMat	Similarity Matrices
ProfDCA.EvoWeaver	Phylogenetic Profiling Predictions for EvoWeaver

-- R --

RandForest	Classification and Regression with Random Forests
RandForest.fit	Classification and Regression with Random Forests
RejectionBy	Given an object of candidate pairs, reject false positives.
RFDist	Robinson-Foulds Distance
RPContextTree.EvoWeaver	Phylogenetic Structure Predictions for EvoWeaver
RPMirrorTree.EvoWeaver	Phylogenetic Structure Predictions for EvoWeaver

-- S --

SelectByK	Predicted pair trimming using K-means.
SequenceInfo.EvoWeaver	Sequence Level Predictions for EvoWeaver
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	EvoWeaver: Identifying Gene Functional Associations from Coevolutionary Signals
SpeciesTree.EvoWeaver	EvoWeaver: Identifying Gene Functional Associations from Coevolutionary Signals
subset.dendrogram	Subsetting dendrogram objects
SubSetPairs	Subset a "PairSummaries" object.
SummarizePairs	Provide summaries of hypothetical orthologs.
SuperTree	Create a Species Tree from Gene Trees
SuperTreeEx	Example Dendrograms

-- T --

TreeDistance.EvoWeaver

Phylogenetic Structure Predictions for EvoWeaver

-- W --

WithinSetCompetition

Pare down candidate pairs to one-to-one sets.

-- misc --

[.LinkedPairs

Tables of where syntenic hits link pairs of genes