Man pages for hemstrow/snpR
Whole-Genome Analysis Tools for Use with Single Nucleotide Polymorphism Data
| calc_abba_baba | Conduct an ABBA/BABA test for gene flow. |
| calc_association | Run case/control or quantitative association tests on SNP... |
| calc_basic_snp_stats | Calculate basic SNP statistics |
| calc_directionality | Calculate the directionality index from a 2d site frequency... |
| calc_fis | Calculate FIS for individual populations. |
| calc_fst | FST from SNP data. |
| calc_genetic_distances | Calculate genetic distances between individuals or groups of... |
| calc_isolation_by_distance | Calculate Isolation by Distance |
| calc_ne | Calculate effective population size. |
| calc_origin_of_expansion | Estimate the origin point of a population expansion using... |
| calc_pairwise_ld | Pairwise LD from SNP data. |
| calc_p_from_bootstraps | Calculate p-values from bootstrapped distributions. |
| calc_prop_poly | Calculate the proportion of polymorphic loci. |
| calc_seg_sites | Calculate the number of segregating sites. |
| calc_sfs | Generate a 1-2d site frequency spectrum from a snpRdata... |
| calc_single_stats | Calculate standard single-SNP genetic statistics |
| calc_smoothed_averages | Gaussian smooth or average statistics across sliding windows. |
| calc_tajimas_d | Tajima's D from SNP data. |
| calc_tree | Generate phylogenetic-like clustering trees. |
| check_duplicates | Checks for duplicated samples in snpRdata. |
| citations | Gather citations for methods used with a snpRdata object |
| colony_interface | Interfaces with the COLONY pedigree assignment program. |
| cross_validate_genomic_prediction | Run a single cross-validation with BGLR. |
| do_bootstraps | Generate bootstrapped windowed statistics |
| extract_snpRdata | Get from or overwrite components of a snpRdata object |
| Facets_in_snpR | Facets in snpR |
| filters | Report on filters used on a snpRdata object. |
| filter_snps | Filter SNPs in snpRdata objects. |
| format_snps | Re-format SNP data. |
| gap_snps | Filter down to one SNPs every _n_ bases. |
| gaussian_weight | Calculate gaussian weights. |
| get.snpR.stats | Pull calculated statistics from snpRdata objects. |
| import.snpR.data | Import genotype and metadata into a snpRdata object. |
| individual_heterozygosity | Calculate individual based heterozygosity. |
| is.snpRdata | Check if an object is a snpRdata object. |
| make_SFS | Generate a 1-2d site frequency spectrum from a dadi input... |
| merge_snpRdata | Merge two snpRdata objects |
| plot_clusters | PCA, tSNE, and umap plots from snpRdata. |
| plot_diagnostic | Basic diagnostic plots |
| plot_manhattan | Generate a manhattan plot from snpRdata or a data.frame. |
| plot_pairwise_fst_heatmap | Make an heatmap of pairwise Fst values. |
| plot_pairwise_ld_heatmap | Create a heatmap from pairwise linkage data. |
| plot_qq | Generate qq plots from p values |
| plot_sfs | Plot 1 or 2d site frequency spectra. |
| plot_structure | Create STRUCTURE-like cluster plots |
| plot_structure_map | Plot STRUCTURE like results on a map. |
| run_genomic_prediction | Interface with BGLR to run genomic prediction with snpRdata... |
| run_random_forest | Run a RANGER random forest using snpRdata for a given... |
| run_sequoia | Run Sequoia pedigree/parentage assignment with snpR |
| show-snpRdata-method | Display snpRdata objects |
| snpRdata-class | Storage class for snpR data and calculated statistics. |
| snpRdata_dims | Get the dimensions of a snpRdata object |
| snpR_import_wrappers | snpRdata Import Wrappers |
| steelMSATs | Siletz Steelhead microsatellite snpRdata |
| steelRAW | Contains example data for 13 microsatellite loci from 1573... |
| stickPED | An artificial pedigree from the stickleback dataset. |
| stickRAW | Deschutes stickleback raw data. |
| stickSNPs | Deschutes stickleback example snpRdata. |
| subset_snpRdata | Subset snpRdata objects |
| summarize_facets | Summarize possible snpRdata object facet options |
| tabulate_allele_frequency_matrix | Fetch the allele frequencies for all SNPs for each level of... |
| vcf_format_utils | Utilities for direct vcf file conversion |
