Manipulate and Visualize VCF Data
AD_frequency
Populate the ID column of VCF data
Check that INFO and FORMAT keys are unique
Convert chrom objects to vcfR objects
Plot chromR object
chromR class
chromR-method
chromR_functions
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
Reformat INFO data as a data.frame
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 gt slot
Query the META section of VCF data
Ranking variants within windows
Create non-overlapping positions (POS) for VCF data
Write summary tables from chromR objects
vcfR class
show
vcfR: Manipulate and Visualize VCF Data
Convert vcfR objects to other formats
Convert vcfR objects to tidy data frames
Convert vcfR to DNAbin
Convert a vcfR object to hapmap
Convert a vcfR object to MigrateN input file
Create window summaries of data
Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.