inst/doc/restfulSE.R

In restfulSE: Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface

## ----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) 

## ----gettx--------------------------------------------------------------------
tenx100k = se100k()
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()
tag = names(AnnotationHub::query(ehub, "tasicST6"))
tasicST6 = ehub[[tag[1]]]
tasicST6

## ----lkd----------------------------------------------------------------------
library(restfulSE)
#data("banoSEMeta", package = "restfulSEData")
ehub = ExperimentHub::ExperimentHub()
tag = names(AnnotationHub::query(ehub, "banoSEMeta"))
banoSEMeta = ehub[[tag[1]]]
banoSEMeta