VariantFiltering (version 1.8.1)

VariantFilteringResults-class: VariantFilteringResults class

Description

The VariantFilteringResults class is used to store the kind of object obtained as a result of an analysis using the functions unrelatedIndividuals(), autosomalRecessiveHomozygous(), autosomalRecessiveHeterozygous(), autosomalDominant(), deNovo() and xLinked(). Its purpose is to ease the task of filtering and prioritizing the variants annotated by those functions.

Details

Variants are stored within a VariantFilteringResults object using a VRanges object, which also holds the variant annotations in its metadata columns. VariantFiltering adds the following core set of annotations. [object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Examples

library(VariantFiltering)

CEUvcf <- file.path(system.file("extdata", package="VariantFiltering"),
                    "CEUtrio.vcf.gz")
CEUped <- file.path(system.file("extdata", package="VariantFiltering"),
                    "CEUtrio.ped")
param <- VariantFilteringParam(vcfFileNames=CEUvcf, pedFileName=CEUped)
reHo <- autosomalRecessiveHomozygous(param)
naMAF(reHo) <- FALSE
maxMAF(reHo) <- 0.05
reHo
head(filteredVariants(reHo))
reportVariants(reHo, type="csv", file="reHo.csv")