deNovo: De Novo variants analysis

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

Description

This function has been created in order to search and annotate de novo variants in one individual, discarding the ones shared with his/her parents.

Usage

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## S4 method for signature 'VariantFilteringParam'
deNovo(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.

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 autosomalRecessiveHeterozygous xLinked VariantFilteringResults

Examples

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## 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)
deNo <- deNovo(param)
deNo

## End(Not run)

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