read.vcfR and write.vcf.
Input of vcf format data results in an S4 object of class vcfR-class.
Objects of class vcfR can be manipulated with vcfR-methods and extract.gt.
Contents of the vcfR object can be visualized with the plot.vcfR method.
More complex visualizations can be created using a series of functions.
See vignette(topic="sequence_coverage") for an example.
Once manipulations are complete the object may be written to a *.vcf.gz format file using write.vcf or exported to objects supported by other R packages with vcfR2genind or vcfR2loci.
More complex visualization can be accomplished by converting a vcfR object to an object of class chromR-class.
An example exists on the create.chromR man page.
The complete list of functions can be displayed with: library(help = vcfR) or by clicking on the 'index' link at the bottom of the page.
Vignettes can be listed with: browseVignettes('vcfR').