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Population Genomics with R


Heredity, Genetics, and GenomicsPrinciples of Population GenomicsUnitsGenome StructuresMutationsDrift and SelectionR Packages and ConventionsRequired Knowledge and Other ReadingsSamples and Sampling DesignsHow Much DNA in a Sample?Degraded SamplesSampling DesignsLow-Throughput TechnologiesGenotypes From PhenotypesDNA Cleavage MethodsRepeat Length PolymorphismSanger and Shotgun SequencingDNA Methylation and Bisulfite SequencingHigh-Throughput TechnologiesDNA MicroarraysHigh-Throughput SequencingRestriction Site Associated DNARNA SequencingExome SequencingSequencing of Pooled IndividualsDesigning a Study With HTSThe Future of DNA SequencingFile FormatsData FilesArchiving and CompressionBioinformatics and GenomicsManaging Read Alignments With RsamtoolsSimulation of High-Throughput Sequencing DataExercises: Genomic Data in RWhat is an R Data Object?Data Classes for Genomic DataThe Class "loci" (pegas)The Class "genind" (adegenet)The Classes "SNPbin" and "genlight" (adegenet)The Class "SnpMatrix" (snpStats)The Class "DNAbin" (ape)The Classes "XString" and "XStringSet" (Biostrings)Data Input and OutputReading Text FilesReading Spreadsheet FilesReading VCF FilesReading PED and BED FilesReading Sequence FilesReading Annotation FilesWriting FilesInternet DatabasesManaging Files and ProjectsExercises: Data ManipulationBasic Data Manipulation in RSubsetting, Replacement, and DeletionCommonly Used FunctionsRecycling and CoercionLogical VectorsMemory ManagementConversionsCase StudiesMitochondrial Genomes of the Asiatic Golden CatComplete Genomes of the Fruit FlyHuman GenomesInfluenza H1N1 Virus SequencesJaguar MicrosatellitesBacterial Whole Genome SequencesMetabarcoding of Fish CommunitiesExercises: Data Exploration and SummariesGenotype and Allele FrequenciesAllelic RichnessMissing DataHaplotype and Nucleotide DiversityThe Class "Haplotype"Haplotype and Nucleotide Diversity From DNA Se-quencesGenetic and Genomic DistancesTheoretical BackgroundHamming DistanceDistances From DNA SequencesDistances From Allele SharingDistances From MicrosatellitesSummary by GroupsSliding WindowsDNA SequencesSummaries With Genomic PositionsPackage SNPRelateMultivariate MethodsMatrix DecompositionEigendecompositionSingular Value DecompositionPower Method and Random MatricesPrincipal Component AnalysisAdegenetFlashpcaRMultidimensional ScalingCase StudiesMitochondrial Genomes of the Asiatic Golden CatComplete Genomes of the Fruit FlyHuman GenomesInfluenza H1N1 Virus SequencesJaguar MicrosatellitesBacterial Whole Genome SequencesMetabarcoding of Fish CommunitiesExercises: Linkage Disequilibrium and Haplotype StructureWhy Linkage Disequilibrium is Important?Linkage Disequilibrium: Two LociPhased GenotypesTheoretical BackgroundImplementation in PegasUnphased GenotypesMore Than Two LociHaplotypes From Unphased GenotypesThe Expectation–Maximization AlgorithmImplementation in haplo.statsLocus-Specific ImputationMaps of Linkage DisequilibriumSNPRelatesnpStatsCase StudiesComplete Genomes of the Fruit FlyHuman GenomesJaguar MicrosatellitesExercises: Population Genetic StructureHardy–Weinberg EquilibriumF-StatisticsTheoretical BackgroundImplementations in pegas and in mmodImplementations in snpStats and in SNPRelateTrees and NetworksMinimum Spanning Trees and NetworksStatistical ParsimonyMedian NetworksPhylogenetic TreesMultivariate MethodsPrinciples of Discriminant AnalysisDiscriminant Analysis of Principal ComponentsClusteringMaximum Likelihood MethodsBayesian ClusteringAdmixtureLikelihood MethodPrincipal Component Analysis of CoancestryA Second Look at F-StatisticsCase StudiesMitochondrial Genomes of the Asiatic Golden CatComplete Genomes of the Fruit FlyInfluenza H1N1 Virus SequencesJaguar MicrosatellitesExercises: Geographical StructureGeographical Data in RPackages and ClassesCalculating Geographical DistancesA Third Look at F-StatisticsHierarchical Components of Genetic DiversityAnalysis of Molecular VarianceMoran I and Spatial AutocorrelationSpatial Principal Component AnalysisFinding Boundaries Between PopulationsSpatial Ancestry (tess3r)Bayesian Methods (Geneland)Case StudiesComplete Genomes of the Fruit FlyHuman GenomesExercises: Past Demographic EventsThe CoalescentThe Standard CoalescentThe Sequential Markovian CoalescentSimulation of Coalescent DataEstimation of ΘHeterozygosityNumber of AllelesSegregating SitesMicrosatellitesTreesCoalescent-Based InferenceMaximum Likelihood MethodsAnalysis of Markov Chain Monte Carlo OutputsSkyline PlotsBayesian MethodsHeterochronous SamplesSite Frequency Spectrum MethodsThe Stairway MethodCubSFSPopsicleWhole-Genome Methods (psmcr)Case StudiesMitochondrial Genomes of the Asiatic Golden CatComplete Genomes of the Fruit FlyInfluenza H1N1 Virus SequencesBacterial Whole Genome SequencesExercises: Natural SelectionTesting NeutralitySimple TestsSelection in Protein-Coding SequencesSelection ScansA Fourth Look at F-StatisticsAssociation Studies (LEA)Principal Component Analysis (pcadapt)Scans for Selection With Extended HaplotypesFST OutliersTime-Series of Allele FrequenciesCase StudiesMitochondrial Genomes of the Asiatic Golden CatComplete Genomes of the Fruit FlyInfluenza H1N1 Virus SequencesExercisesA: Installing R PackagesB: Compressing Large Sequence FilesC: Sampling of Alleles in a PopulationD: GlossaryBibliographyIndex
 
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