Man pages for olli0601/Phyloscanner.R.utilities

phsc.bam.get.length.and.pos.of.mergedreadsCalculate position and length of merged reads
phsc.cmd.bam.calculate.read.distributionGenerate bash commands to calculate read distribution in bam...
phsc.cmd.phyloscanner.multiGenerate bash commands for multiple phyloscanner runs
phsc.cmd.phyloscanner.oneGenerate bash command for a single phyloscanner run
phsc.cmd.phyloscanner.one.resumeGenerate bash command to resume a single phyloscanner run
phsc.cmd.phyloscanner.one.resume.combinewindowsGenerate bash command to combine single window resumes of a...
phsc.cmd.phyloscanner.one.resume.onewindowGenerate bash command to resume a single window of a...
phsc.cmd.process.phyloscanner.output.in.directoryGenerate bash commands to process phyloscanner output
phsc.define.stage1.analysesDetermine stage 1 phyloscanner runs
phsc.find.bam.and.referencesFind bam and corresponding reference files
phsc.find.linked.pairsFind pairs of individuals between whom linkage is not...
phsc.find.transmission.networks.from.linked.pairsFind phylogenetic transmission networks
phsc.get.assignments.by.window.for.coupleGet transmission assignments per window
phsc.get.basic.pairwise.relationshipsCalculate basic pairwise relationships
phsc.get.most.likely.transmission.chainsReconstruct most likely transmission chains
phsc.get.most.likely.transmission.chains.greedyReconstruct most likely transmission chains, greedy algorithm
phsc.get.most.likely.transmission.chains.RBGLedmondsConstruct maximum probability transmission network
phsc.get.pairwise.relationshipsCalculate pairwise relationships
phsc.get.pairwise.relationships.keff.and.neffCount observed relationship states
phsc.get.pairwise.relationships.likelihoodsWrapper script to calculate pairwise relationships and...
phsc.get.pairwise.relationships.posteriorCalculate marginal posterior probability for two individuals...
phsc.get.prior.parameter.n0Calculate prior parameter n0
phsc.plot.default.colours.for.relationtypesDefault colours for relationship types
phsc.plot.maxedge.networkPlot probability network with most likely edges
phsc.plot.most.likely.transmission.chainPlot most likely transmission chain
phsc.plot.phycollapsed.selected.individualsPlot short read phylogenies and highlight individuals
phsc.plot.phyloscanPlot phyloscan
phsc.plot.phy.selected.individualsPlot short read phylogenies and highlight individuals
phsc.plot.phy.selected.pairsPlot all short read phylogenies including two individuals
phsc.plot.transmission.networkPlot transmission network
phsc.plot.windowassignments.by.runsCompare window assignments by different phyloscanner runs
phsc.plot.windowsummaries.for.pairsPlot window summaries for pairs of individuals
phsc.read.likelytransmissionsRead likely transmissions summary files into a data.table
phsc.read.processed.phyloscanner.output.in.directoryRead processed phyloscanner output
phsc.read.subtreesRead subtree information
phsc.read.treesRead short read trees
raxml.cmdGenerate bash commands to generate phylogenies with RAxML
olli0601/Phyloscanner.R.utilities documentation built on Nov. 15, 2018, 11:56 p.m.