The Bioconductor Project Paula Andrea Martinez, PhD. Data Scientist - - PowerPoint PPT Presentation

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the bioconductor project

The Bioconductor Project Paula Andrea Martinez, PhD. Data Scientist - - PowerPoint PPT Presentation

Jul 01, 2023 225 likes •445 views

DataCamp Introduction to Bioconductor INTRODUCTION TO BIOCONDUCTOR The Bioconductor Project Paula Andrea Martinez, PhD. Data Scientist DataCamp Introduction to Bioconductor Bioconductor [1] Bioconductor (www.bioconductor.org) DataCamp

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DataCamp Introduction to Bioconductor

The Bioconductor Project

INTRODUCTION TO BIOCONDUCTOR

Paula Andrea Martinez, PhD.

Data Scientist

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DataCamp Introduction to Bioconductor

Bioconductor

[1] Bioconductor (www.bioconductor.org)

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What do we measure and why?

Structure: elements, regions, size, order, relationships Function: expression, levels, regulation, phenotypes

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How to install Bioconductor packages?

Biconductor has its own repository, way to install packages, and each release is designed to work with a specific version of R. For this course, you'll be using Bioconductor version 3.6. Bioconductor version 3.7 or earlier uses BiocLite: Bioconductor version 3.8 and later uses BiocManager:

source("https://bioconductor.org/biocLite.R") biocLite("packageName") if (!requireNamespace("BiocManager")) install.packages("BiocManager") BiocManager::install()

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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()

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Let's practice!

INTRODUCTION TO BIOCONDUCTOR

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The Role of S4 in Bioconductor

INTRODUCTION TO BIOCONDUCTOR

Paula Andrea Martinez, PhD.

Data Scientist

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S3

Positive CRAN, simple but powerful Flexible and interactive Uses a generic function Functionality depends on the first argument Example: plot() and methods(plot) Negative Bad at validating types and naming conventions (dot not dot?) Inheritance works, but depends on the input

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S4

Positive Formal definition of classes Bioconductor reusability Has validation of types Naming conventions Example: mydescriptor <- new("GenomeDescription") Negative Complex structure compared to S3

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Is it S4 or not?

Ask if an object is S4

str of S4 objects start with Formal class

isS4(mydescriptor) [1] TRUE str(mydescriptor) Formal class 'GenomeDescription' [package "GenomeInfoDb"] with 7 slots ...

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S4 class definition

A class describes a representation name slots (methods/fields) contains (inheritance definition) Example

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")

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S4 Accesors

Object summary

.S4methods(class = "GenomeDescription") [1] commonName organism provider providerVersion [5] releaseDate releaseName seqinfo seqnames [9] show toString bsgenomeName showMethods(classes = "GenomeDescription", where = search()) show(myDescriptor) | organism: () | provider: | provider version: | release date: | release name: | --- | seqlengths:

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DataCamp Introduction to Bioconductor

Let's practice!

INTRODUCTION TO BIOCONDUCTOR

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Introducing biology of genomic datasets

INTRODUCTION TO BIOCONDUCTOR

Paula Andrea Martinez, PhD.

Data Scientist

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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)

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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

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Yeast genome

BSgenome annotation package Using accessors

# load the package and store data into yeast library(BSgenome.Scerevisiae.UCSC.sacCer3) yeast <- BSgenome.Scerevisiae.UCSC.sacCer3 #interested in other genomes? available.genomes() # Chromosome number length(yeast) # Chromosome names names(yeast) # Sequence lengths seqlengths(yeast)

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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)

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Let's practice!

INTRODUCTION TO BIOCONDUCTOR