Introducing biology of genomic datasets

Introduction to Bioconductor in R

James Chapman

Curriculum Manager, DataCamp

Organisms of the kingdoms of life

DNA_parts

Genome elements

Genetic information DNA alphabet
A set of chromosomes (highly variable number)
Genes (carry heredity instructions)
- coding and non-coding
Proteins (responsible for specific functions)
- DNA-to-RNA (transcription)
- RNA-to-protein (translation)

Yeast

A single cell microorganism
The fungus that people love ♥
Used for fermentation: beer, bread, kefir, kombucha, bioremediation, etc.
Name: Saccharomyces cerevisiae or S. cerevisiae

Yeast

BSgenome annotation package

# Load the package and store data into yeast
library(BSgenome.Scerevisiae.UCSC.sacCer3)
yeast <- BSgenome.Scerevisiae.UCSC.sacCer3


# Other available genomes
available.genomes()

"BSgenome.Alyrata.JGI.v1"                   
"BSgenome.Amellifera.BeeBase.assembly4"     
"BSgenome.Amellifera.NCBI.AmelHAv3.1"       
"BSgenome.Amellifera.UCSC.apiMel2"          
"BSgenome.Amellifera.UCSC.apiMel2.masked"
...

length(yeast)

names(yeast)

"chrI"    "chrII"   "chrIII"  "chrIV"   "chrV"    "chrVI"   "chrVII" 
"chrVIII" "chrIX"   "chrX"    "chrXI"   "chrXII"  "chrXIII" "chrXIV" 
"chrXV"   "chrXVI"  "chrM"

seqlengths(yeast)

chrI    chrII   chrIII  chrIV    chrV    chrVI   chrVII   chrVIII  chrIX   chrX 
230218  813184  316620  1531933  576874  270161  1090940  562643   439888  745751 
chrXI  chrXII   chrXIII  chrXIV   chrXV    chrXVI   chrM 
666816 1078177  924431   784333   1091291  948066   85779

Get sequences

getSeq(): S4 method for BSgenome

# Select entire genomic sequence
getSeq(yeast)


# Select sequence from chromosome M
getSeq(yeast, "chrM")


# Select first 10 base pairs
getSeq(yeast, end = 10)

Let's practice!

Introduction to Bioconductor in R