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

alleleClusterDistrCompute a matrix for presence of allele clusters based on...
allelicCoMatrixCreate a co-occurrence matrix from allelic PAM
assignPairIDAssign an ID to each pair of alleles or patterns.
betaSignCongruenceCalculate sign congruence of fixed effects (betas) between...
calcAllelicDiveristyPerCountryAllelic diversity per country or any kind of regions
calcGeneFreqCalculate gene frequency
compEdgeOccurCompare similarity between edges' occurrence
compileGraphsCompile graphs in a GraphSet object into a single network...
compPvaluesDraw a scatter plot and histograms to compare p-values from...
corCladeProjEstimating correlations between clades and projections of...
corPatternProjEstimating correlation between an allelic distribution...
countAllelesMapping alleles to genes
countAllelesPerCountryCount alleles per country
countAllelesPerGeneByCountryCount each gene per country using their alleles
countAllelesPerGeneByYearCount each gene per year using their alleles
countAllelesPerYearCount alleles per year
countAMRClassLinksCount the number of links in a network at the level of...
countNeighboursCount neighbours per node
drawHeatMapDraw a heat map for a given variable
evalPLEvaluate evidence of physical linkage for positive...
extractPairedRowsExtract paired and unpaired rows from a data frame.
extractSubgraphsCreating objects of the class "Graph" for subgraphs of a...
findMinIncCladeDetermine the minimal inclusive clades and calculate its...
findMinIncCladeOfStrainsFinding out and summarising the minimal inclusive clade...
findPhysLinkTesting for associations and physical linkage between every...
findSeqSearch for a query sequence against a list of assemblies
getAllelesEarliestAppearanceGet earliest appearance of each allele in a vector
getAllelesPerPatternConverting an allele-pattern data frame into a...
getAssocGenePairFind out rows corresponding to alleles of a given pair of...
getClusterMemberCooccurrenceRetrieving member allele co-occurrence status and strain...
getGeneClassExtracting gene classes from SRST2-formatted allele IDs.
getRowsXYExtract rows matching to a pair of keys k1 and k2.
heatMapPAMheatMapPAM
importAllelicPAMImport the allelic presence-absence matrix (PAM) of bacterial...
importCoreGenomeSNPsImport genotypes of core-genome SNPs
importGeneticPAMImport the genetic presence/absence (p/a) matrix
lmmTesting for associations between occurrence of bacterial...
mergeIddAllelesMerge identically distributed alleles into a single physical...
mkCoocurNetworkConverting a given network into a co-occurrence network
mkFilterTSVMaking a guidance TSV file as an input for the physDist...
mkNetworkCreate network data from association results.
plrFirth's penalised logistic regression
projectSamplesProject samples onto eigenvectors (of positive eigenvalues)...
retrieveAlleleSetInfoRetrive allelic presence/absence information given a vector...
ringPlotPAMMake a ring plot to show presence/absence of genotypes and...
screePlotPCsCalculating proportion of genetic variation captured by each...
showGeneContentDraw a bubble plot and two bar plots to summarise gene and...
summariseCliquesSummarise allele content per clique
summariseDistAttach new columns summarising distance measurements to LMM...
summariseDistsForEdgesSummarise allelic physical distances for edges in an...
summarisePhysDistForClustersSummarising physical distances involving clusters of alleles
tempNetCreating a temporal network from graphs
testForStruEffTesting for random structural effects of sample projections...
tree2CladesDecompose a tree into a presence/absence matrix of samples in...
vertexAttr2SizeMapping a vector of numerics to vertex sizes through a linear...
wanyuac/GeneMates documentation built on March 1, 2019, 11:42 a.m.