Package index • radiator

Basic
`read_strata()`	read strata
`summary_strata()`	Summary of strata
`filter_rad()`	ONE FUNCTION TO RULE THEM ALL
`genomic_converter()`	Conversion tool among several genomic formats
`radiator_pkg_install()`	radiator packages install helper
Working with strata
`read_strata()`	read strata
`summary_strata()`	Summary of strata
`join_strata()`	Join the strata with the data
`individuals2strata()`	Create a strata file from a list of individuals
`change_pop_names()`	Transform into a factor the STRATA column, change names and reorder the levels
`generate_strata()`	Generate strata object from the data
Read
`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
Tidy
`tidy_genomic_data()`	Transform common genomic dataset format in a tidy data frame
`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 object/file
`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.
Filter
`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, heterozygosity and total coverage
`filter_ld()`	GBS/RADseq short and long distance linkage disequilibrium pruning
`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
`reset_filters()`	Reset filters (individuals and markers) in radiator GDS object.
`list_filters()`	List current active filters (individuals and markers) in radiator GDS object.
`sync_gds()`	sync_gds
Detect
`detect_all_missing()`	Detect markers with all missing genotypes
`detect_allele_problems()`	Detect alternate allele problems
`detect_biallelic_markers()`	Detect biallelic data
`detect_biallelic_problems()`	Detect biallelic problems
`detect_duplicate_genomes()`	Compute pairwise genome similarity or distance between individuals to highligh potential duplicate individuals
`detect_genomic_format()`	Used internally in radiator to detect the file format
`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
Sex markers
`sexy_markers()`	sexy_markers finds sex-linked markers and re-assigns sex
Extract
`check_coverage()` `extract_coverage()`	check_coverage
`extract_dart_target_id()`	Extract DArT target id
`extract_genotypes_metadata()`	extract_genotypes_metadata
`extract_individuals_metadata()`	extract_individuals_metadata
`extract_individuals_vcf()`	Extract individuals from vcf file
`extract_markers_metadata()`	extract_markers_metadata
Summarize
`summary_gds()`	summary_gds
`summary_rad()`	Summary statistics for RADseq data
`summary_strata()`	Summary of strata
Write
`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_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 object.
`write_genlight()`	Write a genlight object from a tidy data frame or GDS file or object.
`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 or object.
`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 object.
`write_structure()`	Write a structure file from a tidy data frame
`write_vcf()`	Write a vcf file from a tidy data frame
Utility functions Internal modules
`allele_frequencies()`	Compute allele frequencies per markers and populations
`betas_estimator()`	Estimate \(\beta\)s per population
`calibrate_alleles()`	Calibrate REF and ALT alleles based on count
`change_pop_names()`	Transform into a factor the STRATA column, change names and reorder the levels
`check_pop_levels()`	Check the use of pop.levels, pop.labels and pop.select arguments.
`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
`ibdg_fh()`	FH measure of IBDg
`pi()`	Nucleotide diversity
`private_alleles()`	Find private alleles
`private_haplotypes()`	private haplotypes
`separate_markers()`	Separate markers column into chrom, locus and pos
Run software
`run_bayescan()`	Run BayeScan

Reference

Basic

Working with strata

Read

Tidy

Filter

Detect

Sex markers

Extract

Summarize

Write

Utility functions

Run software