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## ---- echo = FALSE, message = FALSE-------------------------------------------
library(sesame)
library(FlowSorted.Blood.450k)
options(rmarkdown.html_vignette.check_title = FALSE)
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))
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