vcfR

AD_frequency

Reformat INFO data as a data.frame

Populate the ID column of VCF data

Check that INFO and FORMAT keys are unique

chromR class

chromR-method

Example chromR object.

chromR_functions

Convert chrom objects to vcfR objects

Plot chromR object

Create chromR object

dr.plot elements

Extract elements from vcfR objects

Create fasta format output

freq_peak

Plot freq_peak object

Genetic differentiation

Genotype matrix functions

Get elements from the fixed region of a VCF file

Heatmap with barplots

Read and write vcf format files

Query genotypes for heterozygotes

Minor allele frequency

masplit

Ordinate a sample's data

Pairwise genetic differentiation across populations

Convert allele balance peaks to ploidy

Pipe operator

Population genetics summaries

Process chromR object

Query the META section of VCF data

Query the gt slot

Ranking variants within windows

Create non-overlapping positions (POS) for VCF data

Write summary tables from chromR objects

Variant call format files processed with vcfR.

vcfR class

show

Convert vcfR to DNAbin

Convert a vcfR object to MigrateN input file

Convert vcfR objects to other formats

Example data for vcfR.

Test data for vcfR.

Convert vcfR objects to tidy data frames

Example data from the Variant Effect Predictor (VEP).

Create window summaries of data