autosomalRecessiveHomozygous: Autosomal recessive inheritance analysis: Homozygous

Description Usage Arguments Details Value Author(s) References See Also Examples

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

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## S4 method for signature 'VariantFilteringParam'
autosomalRecessiveHomozygous(param,
                                                               svparam=ScanVcfParam(),
                                                               use=c("everything", "complete.obs", "all.obs"),
                                                               includeHomRef=FALSE,
                                                               age.of.onset=999,
                                                               phenocopies=0,
                                                               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.

includeHomRef

logical value specifying whether the homozygous reference genotype determines the affected phenotype (TRUE) or not (FALSE, default).

age.of.onset

numerical value specifying the age of onset at which individuals below that age are set their phenotype to unknown. This argument is currently experimental.

phenocopies

numerical value specifying the maximum fraction of affected individuals not sharing the homozygous genotype.

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.

Details

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

Value

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

Author(s)

Dei M. Elurbe and R. Castelo

References

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

See Also

autosomalRecessiveHeterozygous autosomalDominant xLinked deNovo unrelatedIndividuals VariantFilteringResults

Examples

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## 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(vcfFilename=CEUvcf, pedFilename=CEUped)
reHo <- autosomalRecessiveHomozygous(param)
reHo

## End(Not run)

rcastelo/VariantFiltering documentation built on Feb. 11, 2021, 11:38 p.m.