meffil.plot.genotypes: Plot SNP beta and sample genotype concordances

In perishky/meffil: Efficient algorithms for DNA methylation

Plot SNP beta and sample genotype concordances

Description

Plot SNP beta and sample genotype concordances

Usage

meffil.plot.genotypes(
  qc.objects,
  genotypes = NULL,
  sample.threshold = 0.9,
  snp.threshold = 0.99
)

Arguments

qc.objects	Output from meffil.qc().
genotypes	Optional output from meffil.extract.genotypes(). Sample genotypes are matched to sample qc.objects using colnames(genotypes) and names(qc.objects).
sample.threshold	Concordance threshold below which the Illumina 450K and genetic profiles for a sample are deemed a mismatch (Default: 0.9).
snp.threshold	Concordance threshold below which the Illumina 450K and genetic profiles for a SNP are deemed a mismatch (Default: 0.99).

Value

A list consisting of:

• graphs A list of ggplot2 objects. The first snp.betas plots the beta distributions of each SNP probe in the microarray. The second and third plots are added only if the genotypes parameter is not NULL. The second plot shows the distribution of SNP concordances, and the third plot shows the distribution of sample concordances.

• tabs Contains two data frames if the genotypes parameter is not NULL. The first samples lists the concordances of each sample, the second snps lists the concordances of each SNP.

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