Stat 550 Main page: Spring 2013.

STAT/BIOSTAT 550: Spring 2013
Statistical Genetics I; Discrete Mendelian traits

Instructor: Elizabeth Thompson
Time: MWF 8.30-9.20
Place: THO 211

SOME OF THE INFORMATION ON THIS (AND LINKED) PAGE(S) MAY NOT BE UPDATED FOR 2013

Single nucleotide polymorphisms are discrete Mendelian traits!

Here is the course announcement.
Here will be a draft schedule: only partially updated for this year.
The draft schedule is usually the first place I update and check links.

PLEASE LET ME KNOW ABOUT ANY NON-WORKING LINKS THAT YOU BELIEVE SHOULD BE WORKING.

Course information

Online participation:

In 2008-2010 this class was given as a separate online class. In 2007 and in 2012 it was given as a regular class. This year, the plan is for a combination: there will be a few distance students participating. Audio and lecture slides will be posted. Additionally (probably for the distance students only) the audio and slides from the 2010 online class will also be posted.

Grading:

Course will be graded 30% homework, 30% computing labs, 10% for participation in class summaries and discussions of homeworks/labs, and 30% final project (info posted 4/20,2012). Participation for distance students will be assessed appropriately.
There is no final exam, apart from the project.
Homeworks or labs will be discussed in class (most) Fridays. Also, I will drop your lowest-scoring homework in computing your overall homework score. (But all labs count.)

Office hours

For brief questions, please see me after class. If you need a longer time, please feel free to email for an appointment. Also, feel free to email me questions about course, lab, or homework material -- if the question is relevant to many in the class, I may respond to the class email, including your query. If I do that, I may edit your query.
I am often available 4.00-5.30 Thursdays, B313-C PDLFD -- apologies to BIOST students.

Books

Here is the official UW list for books for this course. See also the course announcement.

None of the books are necessary: some may be helpful.

My book might be most useful (except the relevant bits are mostly in notes I'll provide on the web).
Weir's book is useful.
Ott's book will be very useful for those going on through Stat/Biostat 552, but less so for this first course.
Lange's book is there mainly so we can put a library reserve hold on it. It has some very good bits.

Email

is good, but is NOT an "instant-messaging" system. Note my preferred email is eathomp@uw.edu.

Computing

We will use the Statistics computer statgen.stat.washington.edu machine for this class. It will also be possible to download and install your own copies of software if you prefer.

HERE is some information for 2013

There is quite a bit of Statistical Genetic software installed in the Biostatistics Computers, and this was extensively updated by Kirk Li in 2012.
HERE is a link to StatGen computing page. You will need your UWNet ID to access this page.

Here are some bits and pieces of possible help: they are also linked in the lab docs:

Copying and editing files or use this older vi editor
Strange problems with files out of DOS (Notepad, for example)
Problems with ssh, or graphics windows -- soon!
See also the information in the 2013 information

Course materials

GENETICS BACKGROUND: Elementary introduction to genetics
These web notes were written for undergraduates, by an undergraduate.
But they may be a useful summary review.
STATISTICS BACKGROUND: Here is a summary of likelihood ideas and theory (PDF version). Here is a note about expectations
which may be helpful to those with less probability and statistics background.
Chapter 1.1 to 1.4 (first posted 3/31/2013: updated 4/07/2013; 4/16/2013)
Chapter 1.5 and 1.6 (first posted 4/07/2013; updated 4/16/2013; 4/21/2013).
Old powerpoint from Matthew Stephens about Clark's algorithm and PHASE
Chapter 2.1 to 2.2 (first posted 4/16/2013; updated 4/21/2013)
Chapter 2.3 to 2.4 (first posted 4/23/2013, updated 4/27/2013; 5/05/2013)
COGA summary (posted 4/27/2013)
Chapter 3.1 to 3.2 (first posted 5/05/2013, updated 5/07/2013, 5/12/2013).
Chapter 3.3 to 3.5 (first posted 5/12/2013, updated 5/14; final 5/21/2013).
Chapter 4.1,4.2 (first posted 5/21/2013, updated 5/23)
Chapter 4.3, 4.4 (first posted 5/27/2013, updated 5/30, final 6/04)
Chapter 4.5, 4.6, and bibliography (first posted 6/02/2013, updated 6/04, final 6/06)
Homeworks and Labs
- Week 1: Homework 1 (Posted 3/31/2013). Due after class, Friday April 5
- Week 2: Homework 2 (Posted 3/31/2013) Due after class, Friday April 12.
- Week 3: Homework 3 (Posted 4/11/2013) and Lab 1 (Checked on statgen.stat, 4/10/2013)
  Both due after class, Friday April 19.
- Week 4: No homework; just a lab: Lab 2 (Checked on statgen.stat, 4/18/2013)
  Additional Pedfiddler information (Checked on statgen.stat, 4/18/2013)
  Due after class, Friday April 26.
- Week 5: Homework 4 (Posted 4/25/2013) Due after class, Friday May 3.
- Week 6: Homework 5 (posted May 1, 2013) and Lab 3 (Checked on statgen.stat, 4/30/2013)
  Both due after class, Friday May 10.
- Week 7: Homework 6 (posted May 9, 2013)
- Week 8: Lab 4 (posted May 16, 2013)
- Week 9: Homework 7 (posted May 23, 2013)
- Week 10: Lab 5; (posted May 26, due June 7).
Projects
Information soon. Preliminary information re the final project is posted (May 10, 2013).
The list of papers is posted.
Note the full paper citations are in the last 3 pages of this document.

UW - Statistics: Thursday, 25-Jul-19 Contact: Elizabeth Thompson <eathomp@u.washington.edu>

STAT/BIOSTAT 550: Spring 2013 Statistical Genetics I; Discrete Mendelian traits

Instructor: Elizabeth Thompson Time: MWF 8.30-9.20 Place: THO 211