Man pages for thierrygosselin/radiator
RADseq Data Exploration, Manipulation and Visualization using R
| allele_count | allele_count |
| allele_frequencies | Compute allele frequencies per markers and populations |
| assign_defaults | assign_defaults |
| bayescan_one | bayescan one iteration |
| betas_estimator | Estimate betas per population |
| blacklist_hw | blacklist_hw |
| boxplot_stats | boxplot_stats |
| calibrate_alleles | Calibrate REF and ALT alleles based on count |
| change_pop_names | Transform into a factor the STRATA column, change names and... |
| check_args_class | check_args_class |
| check_dart | check_dart |
| check_header_source_vcf | Check the vcf header and detect vcf source |
| check_pop_levels | Check the use of pop.levels, pop.labels and pop.select... |
| clean_dart_colnames | clean_dart_colnames |
| clean_dart_locus | clean_dart_locus |
| clean_ind_names | Clean individual's names for radiator and other packages |
| clean_markers_names | Clean marker's names for radiator and other packages |
| clean_pop_names | Clean population's names for radiator and other packages |
| compound_assignment_pipe_operator | compound assignment pipe operator |
| compute_maf | compute_maf |
| count_monomorphic | count_monomorphic |
| dart2gds | dart2gds |
| data_info | data_info |
| detect_allele_problems | Detect alternate allele problems |
| detect_all_missing | Detect markers with all missing genotypes |
| detect_biallelic_markers | Detect biallelic data |
| detect_biallelic_problems | Detect biallelic problems |
| detect_dart_format | detect_dart_format |
| detect_duplicate_genomes | Compute pairwise genome similarity or distance between... |
| detect_genomic_format | Used internally in radiator to detect the file format |
| detect_gt | detect_gt |
| detect_het_outliers | Detect heterozygotes outliers and estimate miscall rate |
| detect_microsatellites | Detect microsatellites |
| detect_mixed_genomes | Detect mixed genomes |
| detect_paralogs | Detect paralogs |
| detect_ref_genome | Detect reference genome |
| diagnostic_maf | MA diagnostic |
| distance2tibble | distance2tibble |
| distance_individuals | Distance individuals |
| erase_genotypes | Erase genotypes |
| estimate_m | heterozygotes miscall rate |
| Exposition_pipe_operator | Exposition pipe-operator |
| extract_coverage | check_coverage |
| extract_dart_target_id | Extract DArT target id |
| extract_data_source | extract_data_source |
| extract_dots | extract_dots |
| extract_genotypes_metadata | extract_genotypes_metadata |
| extract_individuals_metadata | extract_individuals_metadata |
| extract_individuals_vcf | Extract individuals from vcf file |
| extract_info_vcf | extract_info_vcf |
| extract_markers_metadata | extract_markers_metadata |
| filter_blacklist_genotypes | Filter dataset with blacklist of genotypes |
| filter_common_markers | Filter common markers between strata |
| filter_coverage | Filter markers mean coverage |
| filter_dart_reproducibility | Filter data based on DArT reproducibility statistics |
| filter_fis | Fis filter |
| filter_genotyping | Filter markers based on genotyping/missing rate |
| filter_het | Heterozygosity filter |
| filter_hwe | Filter markers based on Hardy-Weinberg Equilibrium |
| filter_individuals | Filter individuals based on genotyping/missingness rate,... |
| filter_ld | GBS/RADseq short and long distance linkage disequilibrium... |
| filter_ma | MAC, MAF and MAD filter |
| filter_monomorphic | Filter monomorphic markers |
| filter_rad | ONE FUNCTION TO RULE THEM ALL |
| filter_snp_number | Filter SNP number per locus/read |
| filter_snp_position_read | Filter markers/SNP based on their position on the read |
| filter_whitelist | Filter dataset with whitelist of markers |
| folder_prefix | folder_prefix |
| folder_short | folder_short |
| gds2tidy | gds2tidy |
| generate_filename | Filename radiator |
| generate_folder | generate_folder |
| generate_geno_freq_boundaries | generate_geno_freq_boundaries |
| generate_gt_vcf_nuc | generate_gt_vcf_nuc |
| generate_hzar | generate_hzar |
| generate_markers_metadata | Generate markers metadata |
| generate_squeleton_folders | generate_squeleton_folders |
| generate_stats | generate_stats |
| generate_strata | Generate strata object from the data |
| generate_whitelist | generate_whitelist |
| genome_similarity | genome_similarity |
| genomic_converter | Conversion tool among several genomic formats |
| gt2array | gt2array |
| gt_recoding | gt_recoding |
| haplotype_reconstruction | haplotype_reconstruction |
| hwe_analysis | hwe_analysis |
| ibdg_fh | FH measure of IBDg |
| import_dart | import_dart |
| individual_het | individual_het |
| individuals2strata | Create a strata file from a list of individuals |
| ind_total_reads | ind_total_reads |
| join_rad | join_rad |
| join_strata | Join the strata with the data |
| ld2df | ld2df |
| ld_boxplot | ld_boxplot |
| ld_missing | Prune dataset based on LD and missingness. |
| ld_pruning | Prune dataset based on LD. |
| list_filters | List current active filters (individuals and markers) in... |
| ma_one | ma_one |
| markers_fis | markers_fis |
| markers_genotyped_helper | markers_genotyped_helper |
| markers_het | markers_het |
| merge_dart | Merge DArT files |
| message_func_call | message_func_call |
| minor_allele_stats | minor_allele_stats |
| missing_per_pop | missing_per_pop |
| n | The number of observations in the current group. |
| not_common_markers | not_common_markers |
| parallel_core_opt | parallel_core_opt |
| parse_gds_metadata | parse_gds_metadata |
| pi | Nucleotide diversity |
| pipe | Forward-pipe operator |
| pi_pop | pi_pop |
| pi_rad | pi_rad |
| plot_bayescan | plot_bayescan |
| plot_boxplot_coverage | Figure box plot of coverage summary statistics |
| plot_boxplot_diversity | Box plot of the diversity (Gene and Haplotypes) |
| plot_coverage_imbalance_diagnostic | Visual diagnostic of coverage imbalance |
| plot_density_distribution_coverage | Figure of distribution (histogram) |
| plot_density_distribution_het | Figure density distribution of the observed heterozygosity... |
| plot_density_distribution_maf | Figure density distribution of minor allele frequency (MAF)... |
| plot_distribution_diversity | Density distribution of diversity (Gene and Haplotypes) |
| plot_het_outliers | plot_het_outliers |
| plot_snp_number_loci | Figure of the distribution of SNP per locus before and after... |
| plot_snp_position_read | Figure of the distribution of SNP nucleotide position alond... |
| plot_upset | plot_upset |
| private_alleles | Find private alleles |
| private_haplotypes | private haplotypes |
| radiator_common_arguments | radiator common arguments |
| radiator_dots | radiator_dots |
| radiator_folder | radiator_folder |
| radiator_function_header | radiator_function_header |
| radiator_future | radiator parallel function |
| radiator_gds | radiator gds constructor |
| radiator_gds_skeleton | radiator_gds_skeleton |
| radiator_packages_dep | radiator_packages_dep |
| radiator_parameters | radiator_parameters |
| radiator_pkg_install | radiator packages install helper |
| radiator_question | radiator_question |
| radiator_results_message | radiator_results_message |
| radiator_snakecase | radiator_snakecase |
| radiator_split_tibble | radiator_split_tibble |
| radiator_tic | radiator_tic |
| radiator_toc | radiator_toc |
| rad_long | rad_long |
| rad_wide | rad_wide |
| read_blacklist_genotypes | read blacklist of genotypes |
| read_blacklist_id | read_blacklist_id |
| read_dart | Read and tidy DArT output files. |
| read_plink | Reads PLINK tped and bed files |
| read_rad | Read radiator file ending '.gds, .rad, .gds.rad'. |
| read_strata | read strata |
| read_vcf | Read VCF files and write a GDS file |
| read_whitelist | read whitelist of markers |
| remove_duplicates | Read tidy genomic data file ending .rad |
| replace_by_na | replace_by_na |
| reset_filters | Reset filters (individuals and markers) in radiator GDS... |
| run_bayescan | Run BayeScan |
| separate_gt | separate_gt |
| separate_markers | Separate markers column into chrom, locus and pos |
| sex_markers_plot | sex_markers_plot |
| sexy_markers | sexy_markers finds sex-linked markers and re-assigns sex |
| simulate_genos_from_posterior | simulate_genos_from_posterior |
| split_tibble_rows | split_tibble_rows |
| split_vcf | Split a VCF file |
| split_vec | split_vec |
| strata_haplo | strata_haplo |
| strip_rad | strip_rad |
| subsampling_data | subsampling data |
| summarise_genotypes | summarise genotypes |
| summarize_sex | summarize_sex |
| summary_gds | summary_gds |
| summary_rad | Summary statistics for RADseq data |
| summary_strata | Summary of strata |
| switch_allele_count | switch_allele_count |
| switch_genotypes | switch_genotypes |
| sync_gds | sync_gds |
| tibble_stats | tibble_stats |
| tidy2gds | tidy2gds |
| tidy2wide | tidy2wide |
| tidy_dart_metadata | Import and tidy DArT metadata. |
| tidy_fstat | fstat file to tidy dataframe |
| tidy_genepop | Import genepop file and convert to a tidy dataframe |
| tidy_genind | Tidy a genind object to a tidy dataframe |
| tidy_genlight | Tidy a genlight object to a tidy dataframe and/or GDS... |
| tidy_genomic_data | Transform common genomic dataset format in a tidy data frame |
| tidy_gtypes | Tidy a gtypes object to a tidy dataframe |
| tidy_plink | Tidy PLINK tped and bed files |
| tidy_vcf | Tidy vcf file |
| tidy_wide | Read/Import a tidy genomic data frames. |
| update_bl_individuals | update_bl_individuals |
| update_bl_markers | update_bl_markers |
| update_filter_parameter | update filter parameter file |
| update_radiator_gds | update_radiator_gds |
| vcf_strata | Join stratification metadata to a VCF (population-aware VCF) |
| write_arlequin | Write an arlequin file from a tidy data frame |
| write_bayescan | Write a BayeScan file from a tidy data frame |
| write_betadiv | Write a betadiv file from a tidy data frame |
| write_colony | Write a 'COLONY' input file |
| write_dadi | Write a 'dadi' SNP input file from a tidy data frame. |
| write_fasta | Export FASTA |
| write_faststructure | Write a faststructure file from a tidy data frame |
| write_fineradstructure | Write a fineRADstructure file from a tidy data frame |
| write_gds | Write a GDS object from a tidy data frame |
| write_genepop | Write a genepop file |
| write_genepopedit | Write a genepopedit flatten object |
| write_genind | Write a genind object from a tidy data frame or GDS file or... |
| write_genlight | Write a genlight object from a tidy data frame or GDS file or... |
| write_gsi_sim | Write a gsi_sim file from a data frame (wide or long/tidy). |
| write_gtypes | Write a strataG object from radiator GDS and tidy data file... |
| write_hapmap | Write a HapMap file from a tidy data frame |
| write_hierfstat | Write a hierfstat file from a tidy data frame |
| write_hzar | Write a HZAR file from a tidy data frame. |
| write_ldna | Write a LDna object from a tidy data frame |
| write_maverick | Write a maverick file from a tidy data frame |
| write_pcadapt | Write a pcadapt file from a tidy data frame |
| write_plink | Write a plink tped/tfam file from a tidy data frame |
| write_rad | Write tidy genomic data file or close GDS file |
| write_related | Write a related file from a tidy data frame |
| write_rubias | Write a rubias object |
| write_snprelate | Write a SNPRelate object from a tidy data frame |
| write_stockr | Write a stockR dataset from a tidy data frame or GDS file or... |
| write_structure | Write a structure file from a tidy data frame |
| write_vcf | Write a vcf file from a tidy data frame |
