In vjcitn/lihc450k: A SummarizedExperiment instance with 450k methylation data on TCGA LIHC

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Introduction

The Illumina 450k methylation data for TCGA cohorts are challenging to serialize and load. This vignette illustrates use of remote HDF5 in the HSDS (HDF Object Store) paradigm.

Briefly, use example(loadLIHC450k) to see how it works. For this example

• a low-content SummarizedExperiment is retrieved from AWS S3 and lodged in a BiocFileCache
• a connection is made to a public HDF Object Store (HSDS instance)
• assay(lim) evaluates to a DelayedArray wrapping the numerical data in the store.

On the other hand

lim2 = loadLIHC450k(useHSDS=FALSE)

replaces the step of connecting to HDF Object Store with a retrieval of 1.2GB of HDF5, and lodges this in a BiocFileCache. assay(lim2) then evaluates to the DelayedArray wrapping the local HDF5 array.

vjcitn/lihc450k documentation built on May 26, 2019, 5:35 a.m.