Package index • genometranslator

Core workflow

Read, inspect, and translate genomic data.

read_genome(): Read genomic data
write_genome(): Write genomic data
genome_translator(): Translate genomic data between formats
tidy_genome(): Convert a GDS genome to a tidy table
genome_info(): Summarise genomic data dimensions
genometranslator_dependencies(): Check genometranslator dependencies

Sample metadata and strata

Prepare, validate, summarize, and modify sample groupings.

read_strata(): read strata
summary_strata(): Summary of strata
individuals2strata(): Create a strata file from a list of individuals
generate_strata(): Generate strata object from the data
join_strata(): Join the strata with the data
change_pop_names(): Transform into a factor the STRATA column, change names and reorder the levels
clean_ind_names(): Clean individual's names for genomic workflows
clean_pop_names(): Clean population's names for genomic workflows
check_pop_levels(): Check the use of pop.levels, pop.labels and pop.select arguments.
vcf_strata(): Join stratification metadata to a VCF (population-aware VCF)

Read genomic data

Format-specific readers offering additional control.

read_dart(): Read and tidy DArT output files.
read_fstat(): Read an FSTAT file into a tidy or wide data frame
read_genepop(): Read a Genepop file into a tidy or wide data frame
read_genind(): Read a genind object to a GDS or tidy dataframe
read_genlight(): Read a genlight object into a tidy data frame and/or GDS object/file
read_gtypes(): Read a gtypes object into a tidy data frame
read_plink(): Reads PLINK tped and bed files
read_vcf(): Read VCF files and write a radiator GDS file

Write genomic data

Export genomic data without silently filtering samples or markers.

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, GDS file or object.
write_genome(): Write genomic data
write_gsi_sim(): Write a gsi_sim file from a data frame (wide or long/tidy).
write_gtypes(): Write a strataG gtypes object from GDS or tidy data
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_related(): Write a related file from a tidy data frame
write_rubias(): Write data in rubias format
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

Detect formats and encoding

detect_genomic_format(): Used internally in radiator to detect the file format
detect_dart_format(): detect_dart_format
detect_gt(): detect_gt
detect_biallelic_markers(): Detect biallelic data
detect_indexing() indexing_vcf(): Check and ensure that a VCF is bgzipped and indexed

Work with GDS

genome_gds(): Genome GDS constructor
genome_gds_skeleton(): genome_gds_skeleton
summary_gds(): summary_gds
update_genome_gds(): update_genome_gds
upgrade_genome_gds(): Upgrade a legacy radiator GDS file
sync_gds(): sync_gds
tidy2gds(): tidy2gds
parse_gds_metadata(): parse_gds_metadata
genome_parameters(): Track changes to genomic data
list_filters(): List current active filters in a genometranslator GDS object
reset_filters(): Reset filters (individuals and markers) in radiator GDS object.

DArT utilities

extract_dart_target_id(): Extract DArT TARGET_ID
extract_dart_markers_metadata(): extract_dart_markers_metadata
tidy_dart_metadata(): Import and tidy DArT metadata.

VCF and bcftools utilities

bcftools_require(): Check that bcftools is available
bcftools_exec(): Run a bcftools command and log stderr
detect_indexing() indexing_vcf(): Check and ensure that a VCF is bgzipped and indexed
check_header_source_vcf(): Check a VCF header and detect its source (caller)
extract_individuals_vcf(): Extract individuals from vcf file

Genotype and marker utilities

extract_genotypes_metadata(): extract_genotypes_metadata
extract_individuals_metadata(): extract_individuals_metadata
extract_markers_metadata(): extract_markers_metadata

Whitelists and blacklists

Import lists used to retain or exclude samples and markers.

read_blacklist_id(): read_blacklist_id
read_whitelist(): Read a marker whitelist