podkat (version 1.4.2)

VariantInfo-class: Class VariantInfo

Description

S4 class for storing information about variants

Details

This class extends the class GRanges without adding any extra slots. The main difference is that VariantInfo objects always have a metadata column MAF that contains minor allele frequencies (MAFs). A special summary method allows for computing statistics about MAFs and types of variants. Objects of this class should only be created and manipulated by the constructors and accessors described below, as only these methods ensure the integrity of the created objects. Direct modification of object slots is strongly discouraged!

References

http://www.bioinf.jku.at/software/podkat

See Also

GRanges, readVariantInfo, genotypeMatrix, readGenotypeMatrix

Examples

vcfFile <- system.file("examples/example1.vcf.gz", package="podkat")

## read variant info directly from VCF file
vInfo <- readVariantInfo(vcfFile, omitZeroMAF=FALSE)
vInfo
summary(vInfo)

## read full genotype from VCF file
geno <- readGenotypeMatrix(vcfFile)

## display summary of variant info stored in genotype matrix
summary(variantInfo(geno))