alleleClusterDistr | Compute a matrix for presence of allele clusters based on... |
allelicCoMatrix | Create a co-occurrence matrix from allelic PAM |
assignPairID | Assign an ID to each pair of alleles or patterns. |
betaSignCongruence | Calculate sign congruence of fixed effects (betas) between... |
calcAllelicDiveristyPerCountry | Allelic diversity per country or any kind of regions |
calcGeneFreq | Calculate gene frequency |
comparePvalues | Draw a scatter plot and histograms to compare p-values from... |
compEdgeOccur | Compare similarity between edges' occurrence |
compileGraphs | Compile graphs in a GraphSet object into a single network... |
corCladeProj | Estimating correlations between clades and projections of... |
corPatternProj | Estimating correlation between an allelic distribution... |
countAlleles | Mapping alleles to genes |
countAllelesPerCountry | Count alleles per country |
countAllelesPerGeneByCountry | Count each gene per country using their alleles |
countAllelesPerGeneByYear | Count each gene per year using their alleles |
countAllelesPerYear | Count alleles per year |
countGeneClassLinks | Count the number of links in a network at the level of gene... |
countNeighbours | Count neighbours per node |
drawHeatMap | Draw a heat map for a given variable |
evalPL | Evaluate evidence of physical linkage for positive... |
extractPairedRows | Extract paired and unpaired rows from a data frame. |
extractSubgraphs | Creating objects of the class "Graph" for subgraphs of a... |
findMinIncClade | Determine the minimal inclusive clades and calculate its... |
findMinIncCladeOfStrains | Finding out and summarising the minimal inclusive clade... |
findPhysLink | Testing for associations and physical linkage between every... |
findSeq | Search for a query sequence against a list of assemblies |
getAllelesEarliestAppearance | Get earliest appearance of each allele in a vector |
getAllelesPerPattern | Converting an allele-pattern data frame into a... |
getAssocGenePair | Find out rows corresponding to alleles of a given pair of... |
getClusterMemberCooccurrence | Retrieving member allele co-occurrence status and strain... |
getGeneClass | Extracting gene classes from SRST2-formatted allele IDs. |
getRowsXY | Extract rows matching to a pair of keys k1 and k2. |
heatMapPAM | An expansion of ggtree's gheatmap function for displaying an... |
importAllelicPAM | Import the allelic presence-absence matrix (PAM) of bacterial... |
importCoreGenomeSNPs | Import genotypes of core-genome SNPs |
importGeneticPAM | Import the genetic presence/absence (p/a) matrix |
importPhysicalDists | Importing a table of physical distances as a data frame |
lmm | Testing for associations between occurrence of bacterial... |
mergeIddAlleles | Merging nodes representing identically distributed alleles... |
mkCoocurNetwork | Converting a given network into a co-occurrence network |
mkFilterTSV | Making a guidance TSV file as an input for the physDist... |
mkNetwork | Create network data from association results. |
plr | Firth's penalised logistic regression |
projectSamples | Project samples onto eigenvectors (of positive eigenvalues)... |
retrieveAlleleSetInfo | Retrive allelic presence-absence information given a vector... |
ringPlotPAM | Make a ring plot to show presence-absence of genotypes and... |
screePlotPCs | Calculating proportion of genetic variation captured by each... |
showGeneContent | Draw a bubble plot and two bar plots to summarise gene and... |
summariseCliques | Summarise allele content per clique |
summariseDist | Attach new columns summarising distance measurements to LMM... |
summariseDistsForEdges | Summarise allelic physical distances for edges in an... |
summarisePhysDistForClusters | Summarising physical distances involving clusters of alleles |
tempNet | Creating a temporal network from graphs |
testForStruEff | Testing for random structural effects of sample projections... |
tree2Clades | Decompose a tree into a presence-absence matrix of samples in... |
vertexAttr2Size | Mapping a numeric vector to vertex sizes through a linear... |
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