Workshop description

In this workshop, we will learn about Bioconductor data containers that use lazy data representations and about their application in real data analysis. We will use some real data examples generated from DNA/RNA-seq, to demonstrate the representation and comprehension of large scale (out-of-memory) genomic datasets. The workshop will be mainly instructor-led live demo with completely working examples. Instructions and notes will be included.

Instructors and contact information

• Hervé Pagès, Fred Hutchinson Cancer Research Center, Seattle, WA
• Qian Liu, Roswell Park Comprehensive Cancer Center, Buffalo, NY
• Martin Morgan, Roswell Park Comprehensive Cancer Center, Buffalo, NY

Pre-requisites

• Basic knowledge of R syntax (matrix, array, data.frame, etc.)
• Some familiarity with manipulation of S4 objects in general
• Some familiarity with SummarizedExperiment objects

Learning objectives

• Introduction to DelayedArray objects and related concepts (seed, delayed operations, realization, block-processed operations, in-memory vs on-disk backends, etc...)

• Use VariantExperiment to represent your DNA-seq data.

• Statistical analysis of variant data (VCF) using VariantExperiment.

• Create SQLDataFrame from in-memory data, text format file, and database tables.

• Use SQLDataFrame to represent and manipulate orgdb database tables.

Workshop participation

Students will be using their laptops with internet connection, follow the instructor to read course materials and run through the working code chunks.

Time outline

Activity	Time
DelayedArray and HDF5Array objects	30m
DelayedArray and HDF5Array hands-on	10m
Specialized DelayedArray backends	10m
VariantExperiment	20m
DelayedDataFrame	10m
SQLDataFrame	10m
Future directions	5-10m

R/Bioconductor packages

The workshop makes use of the following packages:

library(DelayedArray)
library(HDF5Array)
library(pryr)
library(DelayedMatrixStats)
library(SummarizedExperiment)
library(gdsfmt)
library(SeqArray)
library(GDSArray)
library(VCFArray)
library(DelayedDataFrame)
library(SQLDataFrame)
library(VariantAnnotation)
library(org.Hs.eg.db)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(DBI)
#> library(VariantExperiment)