Man pages for wanyuac/GeneMates
Analysing association and physical linkage between bacterial genes
| 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... |
