xLinked: X-Linked inheritance analysis

Description

This function identifies variants that appear only in the X chromosome of the unaffected females as heterozygous, don't appear in the unaffected males analyzed and finally are present (as homozygous) in the affected male(s).

Usage

"xLinked"(param, svparam=ScanVcfParam(), use=c("everything", "complete.obs", "all.obs"), 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).

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.

use

character string specifying the policy to apply on missing genotypes when comparing them. This policy can be either '"everything"' (default), '"complete.obs"' or '"all.obs"'. The default policy ('"everything"') will propagate NA truth values using the behavior of the R logical operators, with the exception that when the final truth value associated with a variant is NA, the variant is ultimately discarded.

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 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.

Examples

Run this code

## Not run: 
# 
# ## This actually won't run b/c in this trio de descendant is a female
# 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)
# xlid <- xLinked(param)
# xlid
# ## End(Not run)

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