VariantFiltering (version 1.4.3)

autosomalRecessiveHomozygous: Autosomal recessive inheritance analysis: Homozygous

Description

This function works analyzing the variants of the unaffected individuals storing the common heterozygous ones and comparing them with the common homozygous variants between the affected subjects.

Usage

"autosomalRecessiveHomozygous"(param, BPPARAM=bpparam("SerialParam"))

Arguments

param

A VariantFilteringParam object built from a multisample VCF file with at least one affected individual and zero or more unaffected ones, and from a PED file specyfing the family relationships among individuals as well as their gender and phenotype status (affected or unaffected).

BPPARAM

An VariantFilteringParam object containing VCF file(s). From 1 to 5 independent files for affected individuals and 0 to 5 more for unaffected ones (up to 10 individuals). If the VCF is a multi-sample, it can contain the same amount of individuals divided likewise.

Value

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

Details

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

References

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

See Also

autosomalRecessiveHeterozygous autosomalDominant xLinked deNovo unrelatedIndividuals VariantFilteringResults

Examples

## Not run: 
# library(VariantFiltering)
# 
# CEUvcf <- file.path(system.file("extdata", package="VariantFiltering"),
#                     "CEUtrio.vcf.bgz")
# CEUped <- file.path(system.file("extdata", package="VariantFiltering"),
#                     "CEUtrio.ped")
# param <- VariantFilteringParam(vcfFilenames=CEUvcf, pedFilename=CEUped)
# reHo <- autosomalRecessiveHomozygous(param)
# reHo
# ## End(Not run)