meffil.snp.concordance: Concordance between genotypes and SNP betas

In perishky/meffil: Efficient algorithms for DNA methylation

Concordance between genotypes and SNP betas

Description

genotypes <- meffil.extract.genotypes(raw.filenames) snp.betas <- meffil.snp.betas(qc.objects) meffil.snp.concordance(snp.betas, genotypesrownames(snp.betas),colnames(snp.betas))

Usage

meffil.snp.concordance(
  snp.betas,
  genotypes,
  snp.threshold = 0.99,
  sample.threshold = 0.9
)

Value

Returns a list of two vectors: - one providing concordances between genotypes and SNP betas for matched samples, - a second providing concordances between genotypes and SNP betas for matched SNPs. as well as the genotype matrix derived from 'snp.betas'.

perishky/meffil documentation built on June 9, 2024, 5:59 p.m.