Description Usage Arguments Value
Female chrX genotypes are untouched, as are genotypes on autosomal chromosomes. Males with heterozygous chrX genotypes are left unchanged, as we cannot be sure which genotype is correct. Possibly they should be removed. We also do not alter genotypes within pseduo-autosomal regions.
1 | reformat_chrX_genotypes(vars, geno, ddd_parents)
|
vars |
seqminer::readVCFToListByRange output, list of values, which includes a genotype matrix as "GT", and sample IDs as sampleId. |
geno |
dataframe of biallelic genotypes, one column per individual |
ddd_parents |
information about DDD individuals, including sex |
dataframe of variants, where male allosomal chrX genotypes have been converted to hemizygous genotypes (e.g. "0/0" -> "0").
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