## ---- echo = FALSE, message = FALSE------------------------------------------- library(sesame) library(FlowSorted.Blood.450k) options(rmarkdown.html_vignette.check_title = FALSE) sesameDataCache("HM450") sesameDataCache("EPIC") ssets <- RGChannelSetToSigSets(FlowSorted.Blood.450k[,1:10]) ## ----------------------------------------------------------------------------- sesameQC(ssets[[1]]) ## ----------------------------------------------------------------------------- qc10 <- do.call(rbind, lapply(ssets, function(x) as.data.frame(sesameQC(x)))) qc10$sample_name <- names(ssets) qc10[,c('mean_beta_cg','frac_meth_cg','frac_unmeth_cg','sex','age')] ## ----------------------------------------------------------------------------- library(ggplot2) ggplot(qc10, aes(x = mean_oob_grn, y= mean_oob_red, label = sample_name)) + geom_point() + geom_text(hjust = -0.1, vjust = 0.1) + geom_abline(intercept = 0, slope = 1, linetype = 'dotted') + xlab('Green Background') + ylab('Red Background') + xlim(c(500,1200)) + ylim(c(500,1200)) ## ----warning = FALSE---------------------------------------------------------- library(wheatmap) p1 <- ggplot(qc10) + geom_bar(aes(sample_name, mean_intensity), stat='identity') + xlab('Sample Name') + ylab('Mean Intensity') + ylim(0,18000) + theme(axis.text.x = element_text(angle=90, vjust=0.5, hjust=1)) p2 <- ggplot(qc10) + geom_bar(aes(sample_name, mean_intensity_total), stat='identity') + xlab('Sample Name') + ylab('Mean M+U Intensity') + ylim(0,18000) + theme(axis.text.x = element_text(angle=90, vjust=0.5, hjust=1)) WGG(p1) + WGG(p2, RightOf()) ## ----------------------------------------------------------------------------- ggplot(qc10) + geom_point(aes(InfI_switch_G2R, InfI_switch_R2G)) ## ----------------------------------------------------------------------------- p1 <- ggplot(qc10) + geom_bar(aes(sample_name, num_na_cg), stat='identity') + xlab('Sample Name') + ylab('Number of NAs') + theme(axis.text.x = element_text(angle=90, vjust=0.5, hjust=1)) p2 <- ggplot(qc10) + geom_bar(aes(sample_name, frac_na_cg), stat='identity') + xlab('Sample Name') + ylab('Fraction of NAs (%)') + theme(axis.text.x = element_text(angle=90, vjust=0.5, hjust=1)) WGG(p1) + WGG(p2, RightOf()) ## ----------------------------------------------------------------------------- sset <- sesameDataGet('EPIC.1.LNCaP')$sset qualityRank(sset) ## ----------------------------------------------------------------------------- sset <- sesameDataGet('EPIC.1.LNCaP')$sset annoS <- sesameDataPullVariantAnno_SNP('EPIC','hg19') annoI <- sesameDataPullVariantAnno_InfiniumI('EPIC','hg19') ## output to console head(formatVCF(sset, annoS=annoS, annoI=annoI))