checkSNPs: Check genotype object
In isglobal-brge/snpfier: Get inversion status in predefined regions

Description Usage Arguments Value Examples

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.

1	checkSNPs(SNPobj, checkAlleleFreqs = TRUE)

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

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

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