## ----setup,echo=FALSE,results="hide"--------------------------------------- suppressPackageStartupMessages({ suppressMessages({ library(BiocStyle) library(HumanTranscriptomeCompendium) library(beeswarm) library(SummarizedExperiment) library(DT) }) }) ## ----lklo------------------------------------------------------------------ v = BiocManager::version() if (v >= "3.10") { library(HumanTranscriptomeCompendium) genelev = htx_load() genelev assay(genelev) } ## ----lksi------------------------------------------------------------------ if (v >= "3.10") { sing = grep("single.cell", genelev$study_title, ignore.case=TRUE) length(sing) } ## ----chkspec--------------------------------------------------------------- if (v >= "3.10") { sa = genelev$study_accession[sing] sing2 = sing[-which(duplicated(sa))] length(sing2) datatable(as.data.frame(colData(genelev[,sing2])), options=list(lengthMenu=c(3,5,10,50,100))) } ## ----lkchar---------------------------------------------------------------- if (v >= "3.10") { bulk = genelev[,-sing] kpglio = grep("glioblastoma", bulk$study_title, ignore.case=TRUE) glioGene = bulk[,kpglio] glioGene } ## ----lkmat----------------------------------------------------------------- if (v >= "3.10") { beeswarm(as.matrix(assay( glioGene["ENSG00000138413.13",1:100])), pwcol=as.numeric(factor(glioGene$study_title[1:100])), ylab="IDH1 expression") legend(.6, 15000, legend=unique(glioGene$study_accession[1:100]), col=1:2, pch=c(1,1)) } ## ----dotx, eval=FALSE------------------------------------------------------ # if (v >= "3.10") { # txlev = htx_load(genesOnly=FALSE) # txlev # }