S4 class for storing information about variants
This class extends the class
adding any extra slots. The main difference is that
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!
creates an empty
GRanges object to class
VariantInfo by adding a “MAF” metadata column that
is initialized with
Furthermore, see the help page of
returns a numeric vector with the minor allele frequencies (MAFs).
returns a string with the number of variants and metadata columns
(if any); if the optional argument
details is set to
TRUE, this method computes and prints a summary about the
MAFs and variant types (if available); this variant returns a
list with summarized values.
All other methods, including sub-setting, are inherited from the
Ulrich Bodenhofer email@example.com
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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))
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