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## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----------------------------------------------------------------------------- suppressPackageStartupMessages(library(ExperimentHub)) # Create ExperimentHub instance ehub <- ExperimentHub() # Find HDCytoData datasets ehub <- query(ehub, "HDCytoData") ehub # Retrieve metadata table md <- as.data.frame(mcols(ehub)) head(md, 2) ## ----------------------------------------------------------------------------- suppressPackageStartupMessages(library(HDCytoData)) # Load 'SummarizedExperiment' object using named function Bodenmiller_BCR_XL_SE() # Load 'flowSet' object using named function Bodenmiller_BCR_XL_flowSet() ## ----------------------------------------------------------------------------- # Create ExperimentHub instance ehub <- ExperimentHub() # Find HDCytoData datasets query(ehub, "HDCytoData") # Load 'SummarizedExperiment' object using dataset ID ehub[["EH2254"]] # Load 'flowSet' object using dataset ID ehub[["EH2255"]] ## ----------------------------------------------------------------------------- # Load dataset in 'SummarizedExperiment' format d_SE <- Bodenmiller_BCR_XL_SE() # Inspect object d_SE length(assays(d_SE)) assay(d_SE)[1:6, 1:6] rowData(d_SE) colData(d_SE) metadata(d_SE)