## ---- echo=FALSE, results="hide", message=FALSE------------------------------- require(knitr) opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE) ## ----style, echo=FALSE, results='asis'---------------------------------------- BiocStyle::markdown() ## ----loadlibs, message=FALSE, warning=FALSE----------------------------------- library(FlowSorted.Blood.450k) library(methylCC) library(minfi) library(tidyr) library(dplyr) library(ggplot2) ## ----data-load, message=FALSE------------------------------------------------- # Phenotypic information about samples head(pData(FlowSorted.Blood.450k)) # RGChannelSet rgset <- FlowSorted.Blood.450k[, pData(FlowSorted.Blood.450k)$CellTypeLong %in% "Whole blood"] ## ----run-estimatecc1, message=FALSE------------------------------------------- set.seed(12345) est <- estimatecc(object = rgset) est ## ----run-estimatecc-summaries------------------------------------------------- cell_counts(est) ## ----run-minfi-estimateCellCounts--------------------------------------------- sampleNames(rgset) <- paste0("Sample", 1:6) est_minfi <- minfi::estimateCellCounts(rgset) est_minfi ## ----compare-estimates-------------------------------------------------------- df_minfi = gather(cbind("samples" = rownames(cell_counts(est)), as.data.frame(est_minfi)), celltype, est, -samples) df_methylCC = gather(cbind("samples" = rownames(cell_counts(est)), cell_counts(est)), celltype, est, -samples) dfcombined <- full_join(df_minfi, df_methylCC, by = c("samples", "celltype")) ggplot(dfcombined, aes(x=est.x, y = est.y, color = celltype)) + geom_point() + xlim(0,1) + ylim(0,1) + geom_abline(intercept = 0, slope = 1) + xlab("Using minfi::estimateCellCounts()") + ylab("Using methylCC::estimatecc()") + labs(title = "Comparing cell composition estimates") ## ----sessionInfo, results='markup'-------------------------------------------- sessionInfo()