Lab 1: Introduction to R and Bioconductor

Original Authors: Martin Morgan, Sonali Arora
Presenting Authors: Martin Morgan, Lori Shepherd
Date: 22 July, 2019 Back: Monday labs

This lab has four (five!) parts. Each part consists of informative material followed by short or intermediate length exercises and case studies. The material introduces or refreshes your knowledge of R, and walks through some of the central classes and annotation resources for working with high-throughput sequence data in Bioconductor.

It’s recommended that you choose two or three of the following sections, and spend about 45 minutes to an hour on each. Take time to work through the code in the material as well as the exercises, asking questions of your colleagues and the TAs as needed. If you’re relatively new to R, then consider doing sections 1 and 3. If you’re new to Bioconductor, then skim the second and focus on the third and fourth sections.

Section 1.5 was added during the lectures this morning, representing one idea of ‘fun’!

Download these files:

• ALLphenoData.tsv
• BRFSS-subset.csv
• airway-sample-sheet.csv
• airway-read-counts.csv
• symgo.csv

Choose the material you’d like to cover:

1.1 Introduction to R – Gain confidence working with base R commands and data structures.

1.2 Introduction to tidy R – Gain confidence working with base R commands and data structures.

1.3 Starting an anlysis – Finding R and Bioconductor packages and resources to start an analysis.

1.4 Data Representations – Learn the essentials of Bioconductor data structures

1.5 Annotation – Learn about Bioconductor resources for gene and genome annotation.