Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/19715
Title: Primer to Analysis of Genomic Data Using R
Contributor(s): Gondro, Cedric  (author)orcid 
Publication Date: 2015
DOI: 10.1007/978-3-319-14475-7
Handle Link: https://hdl.handle.net/1959.11/19715
Abstract: Through this book, researchers and students will learn to use R for analysis of large-scale genomic data and how to create routines to automate analytical steps. The philosophy behind the book is to start with real world raw datasets and perform all the analytical steps needed to reach final results. Though theory plays an important role, this is a practical book for graduate and undergraduate courses in bioinformatics and genomic analysis or for use in lab sessions. How to handle and manage high-throughput genomic data, create automated workflows and speed up analyses in R is also taught. A wide range of R packages useful for working with genomic data are illustrated with practical examples. The key topics covered are association studies, genomic prediction, estimation of population genetic parameters and diversity, gene expression analysis, functional annotation of results using publically available databases and how to work efficiently in R with large genomic datasets. Important principles are demonstrated and illustrated through engaging examples which invite the reader to work with the provided datasets. Some methods that are discussed in this volume include: signatures of selection, population parameters (LD, FST, FIS, etc); use of a genomic relationship matrix for population diversity studies; use of SNP data for parentage testing; snpBLUP and gBLUP for genomic prediction. Step-by-step, all the R code required for a genome-wide association study is shown: starting from raw SNP data, how to build databases to handle and manage the data, quality control and filtering measures, association testing and evaluation of results, through to identification and functional annotation of candidate genes. Similarly, gene expression analyses are shown using microarray and RNAseq data. At a time when genomic data is decidedly big, the skills from this book are critical. In recent years R has become the de facto.
Publication Type: Book
Grant Details: ARC/DP130100542
Publisher: Springer International Publishing
Place of Publication: Heidelberg, Germany
ISBN: 9783319144740
9783319144757
Field of Research (FOR): 060405 Gene Expression (incl. Microarray and other genome-wide approaches)
060408 Genomics
060411 Population, Ecological and Evolutionary Genetics
HERDC Category Description: A1 Authored Book - Scholarly
Other Links: http://trove.nla.gov.au/work/193781698
Extent of Pages: 270
Series Name: Use R!
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Appears in Collections:Book
School of Environmental and Rural Science

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