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
chromR functions        chromR_functions
chromR-class            chromR class
chromR2vcfR             Convert chrom objects to vcfR objects
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
getFIX                  Get elements from the fixed region of a VCF
                        file
heatmap.bp              Heatmap with barplots
is_het                  Query genotypes for heterozygotes
maf                     Minor allele frequency
masplit                 masplit
ordisample              Ordinate a sample's data
query.gt                Query the gt slot
queryMETA               Query the META section of VCF data
show,chromR-method      chromR-method
show,vcfR-method        vcfR-method
vcfR                    Variant call format files processed with vcfR.
vcfR-class              vcfR class
vcfR2DNAbin             Convert vcfR to DNAbin
vcfR_example            Example data for vcfR.
vcfR_test               Test data for vcfR.
write.fasta             Create fasta format output
write.var.info          Write summary tables from chromR objects
