Overview of Bioconductor Aedín Culhane aedin@jimmy.harvard.edu http://bcb.dfci.harvard.edu/~aedin http://www.hsph.harvard.edu/research/aedin-culhane

Bioconductor Biannual release (normally April, October) to coincide with R release. Current: Bioconductor 2.9 (release coincide with R 2.14) To install use script on Bioconductor Website source("http://www.bioconductor.org/biocLite.R") biocLite()

Packages Overview BioConductor web site Bioconductor BiocViews Task view Software Annotation Data Experimental Data

What Packages do I need? Specific to you data and analysis pipeline but for examples: Bioconductor Workshops Bioconductor Workflows

Main types of Annotation Packages Gene centric AnnotationDbi packages: Organism: org.Mm.eg.db. Technology/Platform: hgu133plus2.db. GeneSets and Pathway (biology level): GO.db or KEGG.db .db packages can be queried with sql or accessed using annotation package (totable, get, mget) Genome centric GenomicFeatures packages: Transriptome level: TxDb.Hsapiens.UCSC.hg19.knownGene Generic features: Can generate via GenomicFeatures biomaRt: Query web-based `biomart' resource for genes, sequence, SNPs, and etc. See http://www.bioconductor.org/help/course-materials/2011/BioC2011/LabStuff/AnnotationSlidesBioc2011.pdf

Bioconductor resources Mailing List (sign up for daily digest) Documentation, workshop/course material online Slides from talks, pdf of tutorials, R code Help available for each software package Each package MUST contain vignette (howto)‏ Other resources ww.Rseek.org www.r-bloggers.com

Vignette Tutorials, provide worked example of package Required in Bioconductor packages Written in Sweave (Leisch, 2002). LATEX dynamic reports in which R code is embedded and executable All R code in vignette is checked (and executed) by R CMD check http://www.bioconductor.org/docs/vignettes.html library("Biobase") library("GOstats") # Load package of interest openVignette()

S4 classes and ExpressionSet Within Bioconductor, you will encounter packages are structured around S4 object- oriented programming proposed by John Chambers (developer of S) A class provides a software abstraction of a real world object. A method performs an action on a class (Think of a class as a noun, and method as verb)

Object (S4) An object is an instance of a class. Descriptions are stored in slots slotNames(ob1) lists all slots in object, or use str(). To access slots ob1@slotname slotname(ob1), or slot(ob1, “slotname")

Example: ExpressionSet > ALL ExpressionSet (storageMode: lockedEnvironment) assayData: 12625 features, 128 samples element names: exprs protocolData: none phenoData sampleNames: 01005 01010 ... LAL4 (128 total) varLabels: cod diagnosis ... date last seen (21 total) varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' pubMedIds: 14684422 16243790 Annotation: hgu95av2 library(ALL) data(ALL) slotNames(ALL) ALL@phenoData phenoData(ALL) class(ALL) ?ExpressionSet

Method which act on a S4 class showMethods(class= "ExpressionSet") getMethod("write.exprs", "ExpressionSet") Or if you wish to see how the package really works, download and look the source code

Getting Data into R & Bioconductor Aedín Culhane aedin@jimmy.harvard.edu http://www.hsph.harvard.edu/research/aedin-culhane/

Simple Excel SpreadSheet data Simple table read.table() read.csv() scan() However more datatype specialized. See Technologies on BiocViews. http://www.bioconductor.org/packages/release/BiocVi ews.html Large data files. Also see http://www.revolutionanalytics.com

Some common data types Microarray SNP NGS May 2011

A Microarray Overview

Reading Affymetrix Data library(affy) require(affy) # Alternative affybatch <- ReadAffy(celfile.path="[Location of your data]") eSet<-justRMA() May 2011

Sample R code

ExpressionSet Class in R May 2011

Assessing Data Quality May 2011

Public Microarray Data ArrayExpress 21997 Studies (622,617 profiles,) GEO 22,735 Studies (558,074 profiles) Statistics May 2011

R Code May 2011

More on GEOquery require(GEOquery) Let's try to load the GDS810 dataset which contains data on Alzheimer's disease at various stages of severity. GDS810<-getGEO("GDS810") The getGEO function returns an object of class GEOData. You can get a description of this class like this: help("GEOData-class") Meta(GDS810) Columns(GDS810) head(Table(GDS810)) May 2011

Affy SNP Arrays May 2011

Process – Affy SNP Arrays (Oligo package) May 2011

Other Arrays Illumina 2 color spotted arrays Other arrays Lumi package Limma package Other arrays http://www.bioconductor.org/help/workflows/ol igo-arrays/ May 2011

Next Generation Sequencing Data

R Code May 2011

Exercise Install the library GEOquery Download the dataset GSE1297 using getGEO This data will be downloaded as an eSet, so to see the expression data and phenoData, use pData and exprs Use ArrayQualityMetrics to Assess the data quality of these data May 2011

R basics: Getting help To get help help.search(“mean”)‏ help(mean) help.search(“mean”)‏ apropos("mean") example(mean)‏ http://www.bioconductor.org/help/

With thanks to www.bioconductor.org/help/course.../Bioconductor-Introduction-lab.pdf May 2011