API for hemstrow/snpR
Whole-Genome Analysis Tools for Use with Single Nucleotide Polymorphism Data
| Global functions | |
|---|---|
| .add.facets.snpR.data | Source code |
| .apply.snpR.facets | Source code |
| .average_windows | Source code |
| .bind_and_check_num_levs_a1_a2 | Source code |
| .boot_ac | Source code |
| .boot_as | Source code |
| .boot_genepop | Source code |
| .calc_fst | Source code |
| .calc_weighted_stats | Source code |
| .check.installed | Source code |
| .check.snpR.facet.request | Source code |
| .check.snpRdata | Source code |
| .checkQ | Source code |
| .check_calced_stats | Source code |
| .clumppExport | Source code |
| .collectClumppOutput | Source code |
| .console_hline | Source code |
| .convert_2_to_1_column | Source code |
| .fetch.sample.meta.matching.task.list | Source code |
| .fetch.snp.meta.matching.task.list | Source code |
| .fix..call | Source code |
| .format_and_check_numeric | Source code |
| .fwe_correction | Source code |
| .genind.tosnpRdata | Source code |
| .genlight.to.snpRdata | Source code |
| .get.snpR.stats | Source code |
| .get.task.list | Source code |
| .get_dist | Source code |
| .heterozygosity | Source code |
| .ho_func | Source code |
| .interpolate_sn | Source code |
| .is.bi_allelic | Source code |
| .is.qlist | Source code |
| .maf_func | Source code |
| .make_it_quiet | Source code |
| .merge.snpR.stats | Source code |
| .onAttach | Source code |
| .par_checker | Source code |
| .paste.by.facet | Source code |
| .per_all_f_stat_components | Source code |
| .ploidy | Source code |
| .process_FSTAT | Source code |
| .process_genepop | Source code |
| .process_ms | Source code |
| .process_plink | Source code |
| .process_structure | Source code |
| .process_sync | Source code |
| .process_vcf | Source code |
| .quick_grab_cite | Source code |
| .rand_strings | Source code |
| .readQ | Source code |
| .readQBaps | Source code |
| .readQBasic | Source code |
| .readQClumpp | Source code |
| .readQStructure | Source code |
| .readQTess | Source code |
| .readQTess3 | Source code |
| .remove.facets.snpR.data | Source code |
| .richness_parts | Source code |
| .row_specific_gsub | Source code |
| .sanity_check_sfs | Source code |
| .sanity_check_window | Source code |
| .smart.merge | Source code |
| .split.facet | Source code |
| .sub_and_t_1_2_to_A_C | Source code |
| .subset_snpR_data | Source code |
| .summariseQ | Source code |
| .suppress_specific_warning | Source code |
| .tabulateQ | Source code |
| .tabulate_genotypes | Source code |
| .update.sample.stats.with.new.metadata | Source code |
| .update_calced_stats | Source code |
| .update_citations | Source code |
| .update_filters | Source code |
| .vcf_tag_extract | Source code |
| .yell_citation | Source code |
| Facets_in_snpR | Man page |
| [ | Man page |
| [,snpRdata,ANY,ANY,ANY-method | Man page |
| [,snpRdata-method | Man page |
| calc_abba_baba | Man page |
| calc_allelic_richness | Man page |
| calc_association | Man page Source code |
| calc_basic_snp_stats | Man page |
| calc_directionality | Man page Source code |
| calc_fis | Man page |
| calc_fst | Man page |
| calc_genetic_distances | Man page |
| calc_global_fst | Man page Source code |
| calc_he | Man page |
| calc_het_hom_ratio | Man page |
| calc_ho | Man page |
| calc_hs | Man page |
| calc_hwe | Man page |
| calc_isolation_by_distance | Man page |
| calc_maf | Man page Source code |
| calc_ne | Man page |
| calc_origin_of_expansion | Man page Source code |
| calc_p_from_bootstraps | Man page Source code |
| calc_pairwise_fst | Man page Source code |
| calc_pairwise_ld | Man page |
| calc_pi | Man page Source code |
| calc_private | Man page |
| calc_prop_poly | Man page |
| calc_seg_sites | Man page |
| calc_sfs | Man page Source code |
| calc_single_stats | Man page |
| calc_smoothed_averages | Man page Source code |
| calc_tajimas_d | Man page Source code |
| calc_tree | Man page |
| call_colony | Man page Source code |
| check_duplicates | Man page Source code |
| citations | Man page Source code |
| colony_interface | Man page |
| convert_genind | Man page Source code |
| convert_genlight | Man page Source code |
| convert_vcfR | Man page Source code |
| cross_validate_genomic_prediction | Man page Source code |
| dim | Man page |
| dim,snpRdata-method | Man page |
| do_bootstraps | Man page Source code |
| extract_snpRdata | Man page |
| filter_snps | Man page Source code |
| filters | Man page Source code |
| format_snps | Man page Source code |
| gap_snps | Man page Source code |
| gaussian_weight | Man page Source code |
| genotypes | Man page |
| genotypes,snpRdata-method | Man page |
| genotypes<- | Man page |
| genotypes<-,snpRdata-method | Man page |
| get.snpR.stats | Man page Source code |
| import.snpR.data | Man page Source code |
| individual_heterozygosity | Man page |
| is.snpRdata | Man page Source code |
| make_SFS | Man page Source code |
| merge_snpRdata | Man page Source code |
| ncol | Man page |
| ncol,snpRdata-method | Man page |
| nrow | Man page |
| nrow,snpRdata-method | Man page |
| nsamps | Man page |
| nsamps,snpRdata-method | Man page |
| nsnps | Man page |
| nsnps,snpRdata-method | Man page |
| parse_colony | Man page Source code |
| parse_neestimator | Source code |
| plot_clusters | Man page Source code |
| plot_diagnostic | Man page |
| plot_manhattan | Man page Source code |
| plot_pairwise_fst_heatmap | Man page Source code |
| plot_pairwise_ld_heatmap | Man page Source code |
| plot_qq | Man page Source code |
| plot_sfs | Man page Source code |
| plot_structure | Man page Source code |
| plot_structure_map | Man page Source code |
| read_FSTAT | Man page Source code |
| read_delimited_snps | Man page Source code |
| read_genepop | Man page Source code |
| read_ms | Man page Source code |
| read_non_biallelic | Source code |
| read_plink | Man page Source code |
| read_structure | Man page Source code |
| read_vcf | Man page Source code |
| run_colony | Man page Source code |
| run_genomic_prediction | Man page Source code |
| run_neestimator | Source code |
| run_random_forest | Man page Source code |
| run_sequoia | Man page Source code |
| sample.meta | Man page |
| sample.meta,snpRdata-method | Man page |
| sample.meta<- | Man page |
| sample.meta<-,snpRdata-method | Man page |
| show,snpRdata-method | Man page |
| snp.meta | Man page |
| snp.meta,snpRdata-method | Man page |
| snp.meta<- | Man page |
| snp.meta<-,snpRdata-method | Man page |
| snpR_import_wrappers | Man page |
| snpRdata | Man page |
| snpRdata-class | Man page |
| snpRdata_dims | Man page |
| steelMSATs | Man page |
| steelRAW | Man page |
| stickPED | Man page |
| stickRAW | Man page |
| stickSNPs | Man page |
| subset_snpR_data | Man page Source code |
| subset_snpRdata | Man page |
| summarize_facets | Man page Source code |
| tabulate_allele_frequency_matrix | Man page Source code |
| vcf2beagle | Man page |
| vcf2pl | Man page |
| vcf_format_utils | Man page |
| write_colony_input | Man page Source code |
| write_neestimator_inputs | Source code |
