deNovo: De Novo variants analysis
In VariantFiltering: Filtering of coding and non-coding genetic variants

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

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.

## S4 method for signature 'VariantFilteringParam'
deNovo(param,
                                         svparam=ScanVcfParam(),
                                         use=c("everything", "complete.obs", "all.obs"),
                                         BPPARAM=bpparam("SerialParam"))

`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.

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

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

Dei M. Elurbe and R. Castelo

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

autosomalRecessiveHomozygous autosomalDominant autosomalRecessiveHeterozygous xLinked VariantFilteringResults

## 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)