priorBestVariantVcfR: Title

In aschluter/ClinPrior: Disease Gene prioritization

Title

Description

Title

Usage

priorBestVariantVcfR(
  variants,
  sampleName,
  filter = "",
  isCodingVar = TRUE,
  frequenceAR = 0.01,
  frequenceAD = 5e-05,
  GlobalPhenotypicScore,
  assembly = "assembly37",
  processors = 1
)

Arguments

variants	object of class vcfR-class with the patient variants.
sampleName	character name with the patient code as is written in the VCF file.
filter	character name with the desired filter to select the variants. It should be as is written in the FILTER column in the vcf file.
isCodingVar	logical indicating whether to consider only variants in coding regions. Default TRUE.
frequenceAR	numerical value indicating the MAF(minor allele frequence) to filter out the variants in autosomal recessive and X-linked inheritance. Default 0.01
frequenceAD	numerical value indicating the MAF(minor allele frequence) to filter out the variants in autosomal dominant recessive inheritance. Default 0.00005
GlobalPhenotypicScore	matrix with the phenotypic metrics obtained from the MatrixPropagation function.
assembly	Genome assembly used. Default assembly human GRCh37.
processors	Default=1.

Value

data frame with the patient's variants and their associated information classified from most to least likely to be the cause of the patient's phenotype.

Examples

library(vcfR)
patientHPOsFile <- paste(system.file("extdata/example", package = "ClinPrior"),"HPOpatient.txt",sep="/")
HPOpatient <- unique(read.csv(patientHPOsFile, header = FALSE, sep = "\t")[, 1])
Y<-proteinScore(HPOpatient)
ClinPriorGeneScore<-MatrixPropagation(Y,alpha=0.2)

vcfFile = paste(system.file("extdata/example", package = "ClinPrior"),"HG001_GRCh37_1_22_v4.2.1_benchmark.vep01.KCNQ2Met546Thr.vcf.gz",sep="/")
variants <- read.vcfR(vcfFile)
variantsFiltered <- readVCF(sampleName = "HG001",variants=variants)
result = priorBestVariantVcfR(variants = variantsFiltered, sampleName = "HG001",GlobalPhenotypicScore = ClinPriorGeneScore)

aschluter/ClinPrior documentation built on Sept. 27, 2024, 3:46 a.m.