checkSNPs: Check genotype object

Description Usage Arguments Value Examples

View source: R/checkSNPs.R

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

1
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

Examples

1
2
3
4
5
6
## Run method
if(require(VariantAnnotation)){
    vcf <- readVcf(system.file("extdata", "example.vcf", package = "scoreInvHap"), "hg19")
    resList <- checkSNPs(vcf)
    resList
}

isglobal-brge/snpfier documentation built on Feb. 10, 2021, 3:29 a.m.