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課程名稱 |
基因體統計方法導論
Statistical Analysis for Genomic Data |
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開課學期 |
107-2 |
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授課對象 |
生物資源暨農學院 生物統計學組 |
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授課教師 |
劉力瑜 |
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課號 |
Agron5049 |
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課程識別碼 |
621 U6380 |
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班次 |
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學分 |
3.0 |
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全/半年 |
半年 |
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必/選修 |
選修 |
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上課時間 |
星期一6,7,8(13:20~16:20) |
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上課地點 |
農藝304 |
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備註 |
總人數上限：20人 |
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Ceiba 課程網頁 |
http://ceiba.ntu.edu.tw/1072Agron5049_ |
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課程簡介影片 |
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核心能力關聯 |
核心能力與課程規劃關聯圖 |
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課程大綱
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為確保您我的權利,請尊重智慧財產權及不得非法影印
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課程概述 |
本課程主要介紹分析遺傳與基因體資料的一些統計方法，用以萃取其中之訊息，來回答有關生命科學、數量遺傳學或族群遺傳學上的相關問題。
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課程目標 |
學生能閱讀並理解遺傳與基因體相關文獻的基本統計方法，並有辦法進行電腦上機實作演練。 |
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課程要求 |
作業與實習 30%; 期中考 30%; 期末考 40% |
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預期每週課後學習時數 |
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Office Hours |
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指定閱讀 |
(1) Cui, Y., Zhang, F., Xu, J., Li, Z. and Xu, S. (2015) Mapping quantitative trait loci in selected breeding populations: A segregation distortion approach. Heredity, 115, 538–546.
(2) Haley, C.S. and Knott, S.A. (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity, 69, 315–324.
(3) Kao, C.H. (2000) On the differences between maximum likelihood and regression interval mapping in the analysis of quantitative trait loci. Genetics, 156, 855–865.
(4) Kao, C.H. and Zeng, Z.B. (1997) General formulas for obtaining the MLEs and the asymptotic variance-covariance matrix in mapping quantitative trait loci when using the EM algorithm. Biometrics, 53, 653–665.
(5) Lander, E.S. and Botstein, D. (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics, 121, 185–199.
(6) Todd, E.V., Black, M.A. and Gemmell, N.J. (2016) The power and promise of RNA-seq in ecology and evolution. Molecular Ecology, 25, 1224–1241.
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參考書目 |
(1) Genetic Data Analysis II by Bruce S. Weir
(2) Introduction to quantitative genetics by Falconer and Mackay.
(3) Genetics and analysis of quantitative traits by Lynch and Walsh.
(4) Mathematical and Statistical Methods for Genetics Analysis by Lange.
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評量方式
(僅供參考) |
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No. |
項目 |
百分比 |
說明 |
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1. |
Final |
40% |
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2. |
Midterm |
30% |
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3. |
Homework or practice |
30% |
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週次 |
日期 |
單元主題 |
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第1週 |
02/18 |
Introduction |
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第2週 |
02/25 |
Basic concepts in probability models and likelihood theory
<ul> Reading:
<li> Lange1-2.pdf Section 1.1~1.2
<li> R_StatGene1-2.pdf Section 1.2
</ul> |
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第3週 |
03/04 |
Pedigree analysis and gene frequency estimation |
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第4週 |
03/11 |
演講：<ul><li> 講者：Dr. Philip Brune (Syngenta Crop Protection)
<li> 講題：Introduction to Nutritional Composition Studies of Genetically Modified Crops, and Evaluation of the Results
<li> 地點：農藝館 208R
</ul> |
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第5週 |
03/18 |
EM algorithm; practice (I) |
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第6週 |
03/25 |
Linkage analysis (regression): introduction
http://web.tari.gov.tw/csam/CEB/member/publication/7(2)/001.pdf
01A_Lander_1989.pdf
02Haley_1992.pdf |
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第7週 |
04/01 |
Linkage analysis (regression): regression (REG) interval mapping |
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第8週 |
04/08 |
Practice (II) |
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第9週 |
04/15 |
Introduction to Phylogenetics |
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第10週 |
04/22 |
Distance based method |
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第11週 |
04/29 |
Probability based methods |
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第12週 |
05/06 |
Special topic 1: RNA-seq data analysis 1 |
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第13週 |
05/13 |
Special topic 1: RNA-seq data analysis 2
#upgrade R to the newest version
install.packages("installr")
installr::updateR()
# install Bioconductor basic packages
install.packages("BiocManager")
BiocManager::install()
# install "DESeq2"
BiocManager::install("DESeq2")
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第14週 |
05/20 |
RNA-seq data analysis practice |
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第15週 |
05/27 |
<b>No class</b> |
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第16週 |
06/03 |
Special topic 1: Network analysis |
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第17週 |
06/10 |
Special topic 2: segregation distortion |
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