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vcfR (version 1.0.0)

Tools for Working with Variant Call Format ('VCF') Files

Description

Tools for working with variant call format ('VCF') files. Reads in 'VCF', 'GFF' and 'FASTA' data for visualization. Includes tools for filtering and writing to 'VCF' files.

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Version

Monthly Downloads

6,187

Version

1.0.0

License

GPL

Maintainer

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Last Published

February 22nd, 2016

Functions in vcfR (1.0.0)

chromR2vcfR

Convert chrom objects to vcfR objects
chromR-class

chromR class
chromR functions

chromR_functions
heatmap.bp

Heatmap with barplots
Format conversion

Convert vcfR objects to other formats
Genotype matrix functions

Genotype matrix functions
vcfR2DNAbin

Convert vcfR to DNAbin
write.fasta

Create fasta format output
write.var.info

Write summary tables from chromR objects
Ranking

Ranking variants within windows
query.gt

Query the gt slot
read.vcfR

Read and write vcf format files
Windowing

Create window summaries of data
dr plot elements

dr plot elements
show,chromR-method

chromR methods
chromo_plot

Plot chromR object
vcfR-class

vcfR class
Process chromR objects

Process chromR object
vcfR

Variant call format files processed with vcfR.
create.chromR

Create chromR object
vcfR_example

Example data for vcfR.
extract.gt

Extract elements from vcfR objects
show,vcfR-method

vcfR methods