Files in PopGenome

An Efficient Swiss Army Knife for Population Genomic Analyses

R/PopGenread.R R/VCF_split_into_scaffolds.R R/read.ms.output.R R/site_diversity_between.R R/popgen.R R/calc_freqstats.R R/PsPn.R R/splitting.data.R R/read.big.fasta.R R/calc_hwhafsth_FAST.R R/fisherextest.R R/MS.R R/jump.window.transform.R R/locstatsClass.R R/calc_hwhafsth.R R/set.synnonsyn.R R/D_jacknife.R R/Yach.stats.R R/csstatsClass.R R/deletecodongaps.R R/mktest.R R/calc_D.R R/readHapMap.R R/calc_miss.R R/set_gff_info.R R/GEN.R R/get.recomb.R R/my_math.R R/calc_Bd_clr.R R/weighted.jackknife.R R/get_data.R R/GFF_split_into_scaffolds.R R/my_rdirichlet.R R/my_read.nexus.R R/progress.R R/jointfreqdist.R R/set.ref.positions.R R/pair_linkdisequ.R R/probabilities.R R/ehh.R R/genetree.R R/import_export_slim.R R/DATA.R R/get.feature.names.R R/calc_Bd_CLR_table.R R/site_FST.R R/complike.R R/get_gff_info.R R/mismatch.R R/fstcalc.R R/APE_read.nexus.data.R R/snn.R R/calc_diversities.R R/slim.R R/concatenate.regions.R R/PopGplot.R R/hudsonkaplan85rm.R R/parse_gff.R R/GENOME.R R/readMS.R R/readVCFchunkHap.R R/recomb.stats.R R/PG_plot.biallelic.matrix.R R/splitting.data.sep.R R/mult.linkage.stats.R R/DsPsDnPn.R R/Ewens_Watt.R R/split_data_into_GFF_features.R R/read.big.ms.output.R R/intern.calc.R2.R R/calc_sxsfss.R R/readSNP.R R/codontable.R R/BAYESRETURN.R R/fitting_gff.R R/create.PopGenome.method.R R/update_slim.R R/calc_phi_st.R R/calc_BD.R R/testparamsClass.R R/MK.R R/neuttest.R R/my_unique.R R/set.filter.R R/save_load_GENOME.R R/slide.snp.sep.R R/readData.R R/polymorph.R R/haplochi2.r R/zzz.R R/LOAD.R R/calc.fixed.shared.R R/MS_jointfreqdist.R R/get.biallelic.matrix.R R/calcR2.R R/codonise64.R R/delNULLpop.R R/slidingWindow.R R/getsyn.R R/split_data_into_GFF_attributes.R R/checkpoppairs.R R/SNPFST.R R/region.as.fasta.R R/get.individuals.R R/wall99bq.R R/sliding.window.transform.fast.R R/concatenate.classes.R R/plot_cs.R R/gtest.R R/set.outgroup.R R/myReadVCF.R R/freqtest_achaz.R R/get_segsites.R R/get.sweeps.R R/diversity.stats.between.R R/sortmatrix.R R/APE_write.dna.R R/diversity.stats.R R/linkdisequ.R R/split.GFF.R R/count.unknowns.R R/MS_getStats.R R/counthaplotype.R R/get.codons.R R/DsDn.R R/Whop_readVCF.R R/calc_df.R R/concatenate.R R/calc.R2.R R/linkdisequ_FAST.R R/sweeps.stats.R R/readVCF.R R/permute.R R/readVCFchunk.R R/decodonise64.R R/init_coef.R R/introgression.stats.R R/get_fixed_shared.R R/calc_freqstats_FAST.R R/pair_linkdisequ_FAST.R R/calc_RNDmin.R R/check_init_length.R R/parse_HapMap.R R/sliding.window.transform.new.R R/compute_intern_achaz.R R/jack.knife.transform.R R/coalsim.R R/getsynnonsyndiff.R R/calc_FS.R R/getTable.R R/tn93.R vignettes/XXX.pdf vignettes/PopGenomeClasses.pdf vignettes/2Lslide.pdf vignettes/nucFSTvsAll.pdf vignettes/nucFST.pdf vignettes/SFS.pdf vignettes/XYZ.pdf vignettes/GenesTaj.pdf man/MS_getStats.Rd man/readMS.Rd man/linkage.stats-methods.Rd man/GENOME-class.Rd man/get.individuals-methods.Rd man/readData.Rd man/calc.fixed.shared-methods.Rd man/readHapMap.Rd man/vcf_file.Rd man/get_gff_info.Rd man/diversity.stats-methods.Rd man/BayeScanR.Rd man/concatenate.regions.Rd man/set.filter-methods.Rd man/get.biallelic.matrix-methods.Rd man/read.big.fasta.Rd man/show.slots-methods.Rd man/F_ST.stats.2-methods.Rd man/VCF_split_into_scaffolds.Rd man/weighted.jackknife.Rd man/get.status-methods.Rd man/recomb.stats-methods.Rd man/readVCF.Rd man/split_data_into_GFF_attributes.Rd man/mult.linkage.stats.Rd man/snp_file.Rd man/sliding.window.transform-methods.Rd man/calc.R2-methods.Rd man/test.params-class.Rd man/getBayes-methods.Rd man/fasta_file.Rd man/PG_plot.biallelic.matrix.Rd man/get.codons-methods.Rd man/F_ST.stats-methods.Rd man/set.synnonsyn-methods.Rd man/MS.Rd man/set.populations-methods.Rd man/splitting.data-methods.Rd man/Achaz.stats.Rd man/MKT-methods.Rd man/set.outgroup-methods.Rd man/jack.knife.transform-methods.Rd man/PopGplot.Rd man/gff_file.Rd man/count.unknowns-methods.Rd man/create.PopGenome.method.Rd man/codontable.Rd man/neutrality.stats-methods.Rd man/GFF_split_into_scaffolds.Rd man/load.session.Rd man/save.session.Rd man/readSNP.Rd man/introgression.stats.Rd man/PopGenome.Rd man/region.as.fasta.Rd man/detail.stats-methods.Rd man/diversity.stats.between-methods.Rd man/sweeps.stats-methods.Rd man/concatenate.classes.Rd man/set.ref.positions.Rd man/split_data_into_GFF_features.Rd man/get.feature.names.Rd man/Whop_readVCF.Rd inst/doc/An_introduction_to_the_PopGenome_package.pdf inst/doc/Whole_genome_analyses_using_VCF_files.pdf inst/doc/Integration_of_new_Methods.pdf