## ----setup,echo=FALSE,results="hide"--------------------------------------- suppressPackageStartupMessages({ library(restfulSE) library(GO.db) library(org.Hs.eg.db) library(SummarizedExperiment) library(ExperimentHub) library(AnnotationHub) }) ## ----do10x,eval=FALSE------------------------------------------------------ # library(restfulSE) # my10x = se1.3M() # my10x ## ----doanno, eval=FALSE---------------------------------------------------- # 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) }) ## ----dobanoyy-------------------------------------------------------------- library(restfulSE) bigec2 = H5S_source("http://h5s.channingremotedata.org:5000") bigec2 dsmeta(bigec2)[1:2,] # two groups dsmeta(bigec2)[1,2][[1]] # all dataset candidates in group 1 ## ----doba2----------------------------------------------------------------- banref = bigec2[["assays"]] # arbitrary name assigned long ago banref ## ----doba3----------------------------------------------------------------- ehub = ExperimentHub::ExperimentHub() myfiles <- AnnotationHub::query(ehub , "restfulSEData") myfiles[["EH551"]] -> banoSEMeta #data("banoSEMeta", package = "restfulSEData") rbano = RESTfulSummarizedExperiment(banoSEMeta, banref) rbano ## ----doba4----------------------------------------------------------------- rbanoSub = rbano[5:8, c(3:9, 40:50)] assay(rbanoSub) ## ----gettx----------------------------------------------------------------- txdat = bigec2[["tenx_100k_sorted"]] ehub = ExperimentHub::ExperimentHub() myfiles <- AnnotationHub::query(ehub , "restfulSEData") myfiles[["EH552"]] -> st100k #data("st100k", package = "restfulSEData") tenx100k = RESTfulSummarizedExperiment( st100k, txdat ) tenx100k ## ----anno------------------------------------------------------------------ library(org.Mm.eg.db) atab = select(org.Mm.eg.db, keys="GO:0021766", keytype="GO", columns="ENSEMBL") hg = atab[,"ENSEMBL"] length(hgok <- intersect(hg, rownames(tenx100k))) ## ----getdat, cache=TRUE---------------------------------------------------- hipn = assay(tenx100k[hgok,1:4000]) # slow d = dist(t(log(1+hipn)), method="manhattan") proj = Rtsne(d) ## ----plt,fig=TRUE---------------------------------------------------------- plot(proj$Y) ## ----lktas----------------------------------------------------------------- #data("tasicST6", package = "restfulSEData") ehub = ExperimentHub::ExperimentHub() myfiles <- AnnotationHub::query(ehub , "restfulSEData") myfiles[["EH557"]] -> tasicST6 tasicST6 ## ----lkd------------------------------------------------------------------- library(restfulSE) #data("banoSEMeta", package = "restfulSEData") ehub = ExperimentHub::ExperimentHub() myfiles <- AnnotationHub::query(ehub , "restfulSEData") myfiles[["EH551"]] -> banoSEMeta banoSEMeta ## ----doso------------------------------------------------------------------ mys = H5S_source(serverURL="http://h5s.channingremotedata.org:5000") mys ## ----lkg------------------------------------------------------------------- groups(mys) ## ----lkhl------------------------------------------------------------------ lin1 = rhdf5client::links(mys,1) lin1