AD_frequency            AD_frequency
Convert to tidy data frames
                        Convert vcfR objects to tidy data frames
Format conversion       Convert vcfR objects to other formats
Genotype matrix functions
                        Genotype matrix functions
INFO2df                 Reformat INFO data as a data.frame
Process chromR objects
                        Process chromR object
Ranking                 Ranking variants within windows
VCF input and output    Read and write vcf format files
Windowing               Create window summaries of data
addID                   Populate the ID column of VCF data
check_keys              Check that INFO and FORMAT keys are unique
chromR functions        chromR_functions
chromR-class            chromR class
chromR2vcfR             Convert chrom objects to vcfR objects
chromR_example          Example chromR object.
chromo_plot             Plot chromR object
create.chromR           Create chromR object
dr.plot elements        dr.plot elements
extract.gt              Extract elements from vcfR objects
freq_peak               freq_peak
freq_peak_plot          Plot freq_peak object
genetic_diff            Genetic differentiation
getFIX                  Get elements from the fixed region of a VCF
                        file
gt2popsum               Population genetics summaries
heatmap.bp              Heatmap with barplots
is_het                  Query genotypes for heterozygotes
maf                     Minor allele frequency
masplit                 masplit
ordisample              Ordinate a sample's data
pairwise_genetic_diff   Pairwise genetic differentiation across
                        populations
peak_to_ploid           Convert allele balance peaks to ploidy
query.gt                Query the gt slot
queryMETA               Query the META section of VCF data
rePOS                   Create non-overlapping positions (POS) for VCF
                        data
show,chromR-method      chromR-method
show,vcfR-method        show
vcfR-class              vcfR class
vcfR2DNAbin             Convert vcfR to DNAbin
vcfR2hapmap             Convert a vcfR object to hapmap
vcfR2migrate            Convert a vcfR object to MigrateN input file
vcfR_example            Example data for vcfR.
vcfR_test               Test data for vcfR.
vep                     Example data from the Variant Effect Predictor
                        (VEP).
write.fasta             Create fasta format output
write.var.info          Write summary tables from chromR objects
