## ----setup,echo=FALSE,results="hide"------------------------------------------ suppressPackageStartupMessages({ library(restfulSE) library(GO.db) library(org.Hs.eg.db) library(SummarizedExperiment) library(ExperimentHub) library(AnnotationHub) }) ## ----do10x,eval=TRUE---------------------------------------------------------- library(restfulSE) my10x = se1.3M() my10x ## ----doanno, eval=TRUE-------------------------------------------------------- library(org.Mm.eg.db) hippdev = select(org.Mm.eg.db, keys="GO:0021766", keytype="GO", column="ENSEMBL")$ENSEMBL hippdev = intersect(hippdev, rownames(my10x)) #unname(assay(my10x[ hippdev[1:10], 10001:10006])) ## ----lktiss, eval=TRUE-------------------------------------------------------- tiss = gtexTiss() tiss ## ----findbr------------------------------------------------------------------- binds = grep("Brain", tiss$smtsd) table(tiss$smtsd[binds][1:100]) # check diversity in 100 samples ## ----findn-------------------------------------------------------------------- ntgenes = goPatt(termPattern="neurotroph") head(ntgenes) ## ----setup2,echo=FALSE-------------------------------------------------------- suppressPackageStartupMessages({ library(restfulSE) library(SummarizedExperiment) library(Rtsne) library(rhdf5client) }) ## ----doba3-------------------------------------------------------------------- ehub = ExperimentHub::ExperimentHub() tag = names(AnnotationHub::query(ehub, "banoSEMeta")) banoSE = ehub[[tag[1]]] ds = HSDSArray(endpoint=URL_hsds(),svrtype="hsds", domain="/shared/bioconductor/bano_meQTLex.h5",dsetname="/assay001") assays(banoSE, withDimnames=FALSE) = SimpleList(betas=ds) banoSE ## ----doba4-------------------------------------------------------------------- rbanoSub = banoSE[5:8, c(3:9, 40:50)] assay(rbanoSub) ## ----anno,eval=FALSE---------------------------------------------------------- # library(org.Mm.eg.db) # atab = select(org.Mm.eg.db, keys="GO:0021766", keytype="GO", columns="ENSEMBL") # hg = atab[,"ENSEMBL"] # ehub = ExperimentHub::ExperimentHub() # lkst100k = AnnotationHub::query(ehub, "st100k") # tenx100k = ehub[[names(lkst100k)]] # length(hgok <- intersect(hg, rownames(tenx100k))) ## ----getdat, cache=FALSE,eval=FALSE------------------------------------------- # hipn = assay(tenx100k[hgok,1:4000]) # slow # d = dist(t(log(1+hipn)), method="manhattan") # proj = Rtsne(d) ## ----plt,fig=FALSE,eval=FALSE------------------------------------------------- # plot(proj$Y) ## ----lktas-------------------------------------------------------------------- #data("tasicST6", package = "restfulSEData") ehub = ExperimentHub::ExperimentHub() tag = names(AnnotationHub::query(ehub, "tasicST6")) tasicST6 = ehub[[tag[1]]] tasicST6 ## ----lkd---------------------------------------------------------------------- library(restfulSE) ehub = ExperimentHub::ExperimentHub() tag = names(AnnotationHub::query(ehub, "banoSEMeta")) banoSEMeta = ehub[[tag[1]]] banoSEMeta