In perishky/meffil: Efficient algorithms for DNA methylation

There are r sum(!qc.summary$genotype.summary$tabs$snp$is.concordant, na.rm=T) SNP probes whose genotypes do not match their values on the microarray (concordance threshold = r qc.summary$parameters$snp.concordance.threshold). It is recommended to drop this SNP probe before calculating sample concordance.

tab <- qc.summary$genotype.summary$tabs$snps
tab <- tab[which(!tab$is.concordant),]
if (nrow(tab) > 0) kable(tab,row.names=F)

SNP concordances are distributed as follows:

(qc.summary$genotype.summary$graphs$snp.concordance)

There are r sum(!qc.summary$genotype.summary$tabs$samples$is.concordant, na.rm=T) samples whose genotypes do not match the SNP probes on the microarray (concordance threshold = r qc.summary$parameters$sample.genotype.concordance.threshold).

tab <- qc.summary$genotype.summary$tabs$samples
tab <- tab[which(!tab$is.concordant),]
if (nrow(tab) > 0) kable(tab,row.names=F)

Sample concordances are distributed as follows:

(qc.summary$genotype.summary$graphs$sample.concordance)

perishky/meffil documentation built on March 20, 2024, 1:56 a.m.