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)
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