lecture15

Lecture 15: 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, VCF files)
• Identify and annotate genomic variants

Before the class

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

1. Install the R packages

• Tutorial is tested for R-4.0.3
• You will need the Docker container containing the correct version of R and the required R packages already installed.
• This these packages:

  • GenomicRanges: manipulating genomic data

  • plyranges: fast & easy tool for mannipulating GRanges

    ## start R session ##
    R
    ## check that these packages can be loaded successfully ##
    library(tidyverse)
    library(GenomicRanges)
    library(plyranges)
    

2. Class materials: R Markdown and Jupyter Notebook 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 (lecture15) containing the following three R tutorials:
  • R Markdown files
    • Lecture15_GenomicData.Rmd: store genomic data as objects, assess genomic ranges, apply operations on genomic data
    • Lecture15_VariantCalls.Rmd: load and assess variant (vcf) data
  • Jupyter Notebook files
    • Lecture15_GenomicData.ipynb
    • Lecture15_VariantCalls.ipynb

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

• Please download all data files found in this folder and add them to your lecture15 directory. The files should have the following filenames:
  • BRCA.genome_wide_snp_6_broad_Level_3_scna.seg
  • 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