correctAlleleTable: Solve genotypes discrepancies

In isglobal-brge/scoreInvHap: Get inversion status in predefined regions

Description

This function tries to solve discrepancies between the reference and sample genotypes. The cause of these discrepancies is that samples and references have used different strands to codify the SNP. This function get the complement genotypes for the discordant SNPs and checks if discordancies are solved.

Usage

correctAlleleTable(alleletable, hetRefs, map)

Arguments

alleletable	Data.frame with the alleles per SNP (from getAlleleTable)
hetRefs	Character vector with the heterozygous genotypes in the reference.
map	Data.frame with the annotation of the SNPs (from plink format)

Value

alleletable without discrepancies between these genotypes and the references.

isglobal-brge/scoreInvHap documentation built on Feb. 7, 2021, 8:43 a.m.