tfcb_2021

Lecture 16: Genomic data in R

This lecture will unite the last lecture’s content on genomic analysis with our previous coding in R. The packages we’ll use this week are from Bioconductor, a collection of software specifically designed for genomic analysis in R.

Lecture Notes

Lecture slides

Learning objectives

Genome variant analysis (Background)

• Types of genomic variation
• Tools to predict genomic variations
• Learn the common file formats for variation data
• Databases and online resources for human variation data

Genomic Data (hands-on tutorials)

• Use Bioconductor packages to work with genomic data in R
• Load, inspect, and query genomic data (BED/SEG, BAM, VCF files)
• Identify and annotate genomic variants

Before the class

We will be working through some tutorials directly on your laptop using R Studio.

1. Install the R packages

• Tutorial is tested for R-4.0.3
• You should run this script in VSCode to ensure all Bioconductor packages are installed.

    ## start R session ##
    R
    ## run this command within R session ##
    source("../../software/genomic_data.R")
  

• This script will install the following packages:
  • Rsamtools: querying BAM files
  • VariantAnnotation: reading VCF files
  • GenomicRanges: manipulating genomic data
  • plyranges: fast & easy tool for mannipulating GRanges

2. Class materials: R Markdown files containing the tutorials

• If you have not done so already, update your local copy of the class repository from GitHub. You should have a directory (lecture16) containing the following three RMarkdown tutorials:
  • Lecture16_GenomicData.Rmd: store genomic data as objects, assess genomic ranges, apply operations on genomic data
  • Lecture16_Rsamtools.Rmd: load and query sequencing data; compute “pile-up” statistics at genomic loci to identify genomic variants
  • Lecture16_VariantCalls.Rmd: load and assess variant (vcf) data

3. Install R Extension in VSCode

• Extensions (on left panel) > Type in search bar: "R Extension" > Select R Extension for Visual Studio Code by Yuki Ueda
• The extension page should look something like this: https://marketplace.visualstudio.com/items?itemName=Ikuyadeu.r

4. Install pandoc

• To knit R Markdown files, you’ll need the R Extension as well as pandoc.
• Install pandoc outside of VScode by downloading the installer here: https://pandoc.org/installing.html

5. Class materials: Genomic and sequencing data for the tutorials

• Please download all data files found in this folder and add them to your lecture16 directory. The files should have the following filenames:
  • BRCA.genome_wide_snp_6_broad_Level_3_scna.seg
  • BRCA_IDC_cfDNA.bam
  • BRCA_IDC_cfDNA.bam.bai
  • GIAB_highconf_v.3.3.2.vcf.gz (if this file was automatically uncompressed on your computer, resulting in a file named GIAB_highconf_v.3.3.2.vcf, look in your Trash folder to find the original file ending in gz)
  • GIAB_highconf_v.3.3.2.vcf.gz.tbi