## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----install------------------------------------------------------------------ if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("emtdata") ## ----load-packages, message=FALSE--------------------------------------------- library(emtdata) library(ExperimentHub) library(SummarizedExperiment) ## ----get-emtdata-------------------------------------------------------------- eh = ExperimentHub() query(eh , 'emtdata') ## ----download-emtdata-cursons2018-id------------------------------------------ eh[['EH5440']] ## ----download-emtdata-cursons2018-accessor------------------------------------ #metadata are displayed cursons2018_se(metadata = TRUE) #data are loaded cursons2018_se() ## ----access-se---------------------------------------------------------------- cursons2018_se = eh[['EH5440']] #read counts assay(cursons2018_se)[1:5, 1:5] #genes rowData(cursons2018_se) #sample information colData(cursons2018_se) ## ----------------------------------------------------------------------------- library(edgeR) library(RColorBrewer) cursons2018_dge <- asDGEList(cursons2018_se) cursons2018_dge <- calcNormFactors(cursons2018_dge) plotMDS(cursons2018_dge) ## ----------------------------------------------------------------------------- cursons2015_se = eh[['EH5441']] cursons2015_dge <- asDGEList(cursons2015_se) cursons2015_dge <- calcNormFactors(cursons2015_dge) colours <- brewer.pal(7, name = "Paired") plotMDS(cursons2015_dge, dim.plot = c(2,3), col=rep(colours, each = 3)) ## ----------------------------------------------------------------------------- foroutan2017_se = eh[['EH5439']] foroutan2017_dge <- asDGEList(foroutan2017_se, assay_name = "logExpr") foroutan2017_dge <- calcNormFactors(foroutan2017_dge) tgfb_col <- as.numeric(foroutan2017_dge$samples$Treatment %in% 'TGFb') + 1 plotMDS(foroutan2017_dge, labels = foroutan2017_dge$samples$Treatment, col = tgfb_col) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()