autosomalRecessiveHomozygous {VariantFiltering} | R Documentation |
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.
## S4 method for signature 'VariantFilteringParam' autosomalRecessiveHomozygous(param, svparam=ScanVcfParam(), use=c("everything", "complete.obs", "all.obs"), includeHomRef=FALSE, BPPARAM=bpparam("SerialParam"))
param |
A |
svparam |
An instance of a |
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 |
includeHomRef |
logical value specifying whether the homozygous reference genotype determines the affected phenotype ( |
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. |
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.
autosomalRecessiveHeterozygous
autosomalDominant
xLinked
deNovo
unrelatedIndividuals
VariantFilteringResults
## 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)