The Bioconductor
Project
INTRODUCTION TO BIOCONDUCTOR IN R
Paula Andrea Martinez, PhD.
Data Scientist
Bioconductor
1 Bioconductor (www.bioconductor.org)
INTRODUCTION TO BIOCONDUCTOR IN R
What do we measure and why?
Structure: elements, regions, size, order, relationships
Function: expression, levels, regulation, phenotypes
INTRODUCTION TO BIOCONDUCTOR IN R
How to install Bioconductor packages?
Biconductor has its own repository, way to install packages, and each release is designed to
work with a speci c version of R.
For this course, you'll be using Bioconductor version 3.6.
Bioconductor version 3.7 or earlier uses BiocLite:
source("https://bioconductor.org/biocLite.R")
biocLite("packageName")
Bioconductor version 3.8 and later uses BiocManager:
if (!requireNamespace("BiocManager"))
install.packages("BiocManager")
BiocManager::install()
INTRODUCTION TO BIOCONDUCTOR IN R
Bioconductor version and package version
BiocInstaller works for Bioconductor version 3.7 or earlier
# Check Bioconductor version (For versions <= 3.7)
BiocInstaller::biocVersion()
# or
biocVersion()
# Load a package
library(packageName)
# Check versions for reproducibility
sessionInfo()
# or
packageVersion("packageName")
# Check package updates (Bioconductor version <= 3.7)
BiocInstaller::biocValid()
# or
biocValid()
INTRODUCTION TO BIOCONDUCTOR IN R
Let's practice!
INTRODUCTION TO BIOCONDUCTOR IN R
The Role of S4 in
Bioconductor
INTRODUCTION TO BIOCONDUCTOR IN R
Paula Andrea Martinez, PhD.
Data Scientist
S3
Positive
CRAN, simple but powerful
Flexible and interactive
Uses a generic function
Functionality depends on the rst argument
Example: plot() and methods(plot)
Negative
Bad at validating types and naming conventions (dot not dot?)
Inheritance works, but depends on the input
INTRODUCTION TO BIOCONDUCTOR IN R
S4
Positive
Formal de nition of classes
Bioconductor reusability
Has validation of types
Naming conventions
Example: mydescriptor <- new("GenomeDescription")
Negative
Complex structure compared to S3
INTRODUCTION TO BIOCONDUCTOR IN R
Is it S4 or not?
Ask if an object is S4
isS4(mydescriptor)
TRUE
str of S4 objects start with Formal class
str(mydescriptor)
Formal class 'GenomeDescription' [package "GenomeInfoDb"] with 7 slots
...
INTRODUCTION TO BIOCONDUCTOR IN R
S4 class definition
A class describes a representation
name
slots (methods/ elds)
contains (inheritance de nition)
MyEpicProject <- setClass(# Define class name with UpperCamelCase
"MyEpicProject",
# Define slots, helpful for validation
slots = c(ini = "Date",
end = "Date",
milestone = "character"),
# Define inheritance
contains = "MyProject")
INTRODUCTION TO BIOCONDUCTOR IN R
.S4methods(class = "GenomeDescription")
[1] commonName organism provider providerVersion releaseDate releaseName seqinfo
[8] seqnames show toString bsgenomeName
showMethods(classes = "GenomeDescription", where = search())
Object summary
show(myDescriptor)
| organism: ()
| provider:
| provider version:
| release date:
| release name:
| ---
| seqlengths:
INTRODUCTION TO BIOCONDUCTOR IN R
Let's practice!
INTRODUCTION TO BIOCONDUCTOR IN R
Introducing biology
of genomic datasets
INTRODUCTION TO BIOCONDUCTOR IN R
Paula Andrea Martinez, PhD.
Data Scientist
INTRODUCTION TO BIOCONDUCTOR IN R
INTRODUCTION TO BIOCONDUCTOR IN R
Genome elements
Genetic information DNA alphabet
A set of chromosomes (highly variable number)
Genes (carry heredity instructions)
coding and non-coding
Proteins (responsible for speci c functions)
DNA-to-RNA (transcription)
RNA-to-protein (translation)
INTRODUCTION TO BIOCONDUCTOR IN R
Yeast
A single cell microorganism
The fungus that people love ♥
Used for fermentation: beer, bread, ke r,
kombucha, bioremediation, etc.
Name: Saccharomyces cerevisiae or S.
cerevisiae
INTRODUCTION TO BIOCONDUCTOR IN R
BSgenome annotation package
# load the package and store data into yeast
library(BSgenome.Scerevisiae.UCSC.sacCer3)
yeast <- BSgenome.Scerevisiae.UCSC.sacCer3
#interested in other genomes?
available.genomes()
Using accessors
# Chromosome number
length(yeast)
# Chromosome names
names(yeast)
# Sequence lengths
seqlengths(yeast)
INTRODUCTION TO BIOCONDUCTOR IN R
Get sequences
S4 method for BSgenome
# S4 method getSeq() requires a BSgenome object
getSeq(yeast)
# Select chromosome sequence by name, one or many
getSeq(yeast, "chrM")
# Select start, end and or width
# end = 10, selects first 10 base pairs of each chromosome
getSeq(yeast, end = 10)
INTRODUCTION TO BIOCONDUCTOR IN R
Let's practice!
INTRODUCTION TO BIOCONDUCTOR IN R
