autosomalRecessiveHeterozygous: Autosomal recessive inheritance analysis: Heterozygous

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

Description

This function aims to analyze the variants of the unaffected individuals, storing and grouping the heterozygous ones by gene. The affected individuals ought present two or more different heterozygous changes in the gene, and at least one of them shall come from each parent.

Usage

1
2
3
4
## S4 method for signature 'VariantFilteringParam'
autosomalRecessiveHeterozygous(param,
                                                                 svparam=ScanVcfParam(),
                                                                 BPPARAM=bpparam("SerialParam"))

Arguments

param

A VariantFilteringParam object built from a multisample VCF file with at least one affected individual and two 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.

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.

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

autosomalRecessiveHomozygous autosomalDominant xLinked deNovo VariantFilteringResults

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
## Not run: 

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)
reHet <- autosomalRecessiveHeterozygous(param)
reHet

## End(Not run)

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