checkSNPs: Check genotype object

In scoreInvHap: Get inversion status in predefined regions

Description

This function checks the genotype object before passing the SNPs to 'scoreInvHap'. The function removes SNPs with different alleles or different allele frequencies. Nonetheless, it is possible that these SNPs could be recovered after an examination of the results. Be aware that testing of allele frequencies might fail for small datasets.

Usage

checkSNPs(SNPobj, checkAlleleFreqs = TRUE)

Arguments

SNPobj	List with SNPs data from plink or VCF-class.
checkAlleleFreqs	Should allele frequencies be check (Default: TRUE)

Value

List containing the SNPs prepared for scoreInvHap

• genos: Object with genotype data ready for scoreInvHap

• wrongAlleles: Character vector with the SNPs discarded due to having alleles different to reference

• wrongFreqs: Character vector with the SNPs discarded due to having allele frequencies different to reference

Examples

## Run method
if(require(VariantAnnotation)){
    vcf <- readVcf(system.file("extdata", "example.vcf", package = "scoreInvHap"), "hg19")
    resList <- checkSNPs(vcf)
    resList
}

scoreInvHap documentation built on Feb. 6, 2021, 2 a.m.