VariantFiltering (version 1.8.1)

unrelatedIndividuals: Analysis designed to be applied over a group of unrelated individuals

Description

This function is designed to create an object to deepen into the variants presented by a group of unrelated individuals

Usage

## S3 method for class 'VariantFilteringParam':
unrelatedIndividuals(param,
                                                       svparam=ScanVcfParam(),
                                                       BPPARAM=bpparam("SerialParam"))

Arguments

param

A VariantFilteringParam object built from a multisample VCF file.

svparam

An instance of a ScanVcfParam object to enable analyzing a subset of variants and samples. This object is passed internally to a call to the readVcf() function in the VariantAnnotation package, see its help page for a complete description of this functionality.

BPPARAM

An object of class BiocParallelParam specifiying parameters related to the parallel execution of some of the tasks and calculations within this function. See function bpparam() from the BiocParallel package.

Value

• An object of class VariantFilteringResults including functional annotations on all variants.

Details

This function requires as an input a VariantFilteringParam class object built from an input multisample VCF file.

References

Elurbe D.M., Mila, M., Castelo, R. The VariantFiltering package, in preparation.

See Also

autosomalRecessiveHomozygous autosomalRecessiveHeterozygous autosomalDominant deNovo xLinked VariantFilteringResults

Examples

CEUvcf <- file.path(system.file("extdata", package="VariantFiltering"), "CEUtrio.vcf.bgz")
param <- VariantFilteringParam(vcfFilenames=CEUvcf)
uInd <- unrelatedIndividuals(param)
uInd