Announcements
From Cs124
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4/2/2008
- Lecture 1 (Homework 0A) and Lecture 2 have been posted
4/3/2008
- Homework 0 has been posted and is due 4/11/2008 electronically
4/4/2008
- A few typos were discovered in Homework 0 and have been fixed. If you downloaded it last night, please get it again!
4/7/2008
- A few more typos were discovered in Homework 0 and have been fixed. They correspond to problem 4. If you already turned in your homework, the solutions are not very different so it's ok if you don't fix your solutions. If you haven't turned in your homework, we have added a small part to problem 4 that asks you to compute the probability of a linkage landing in a bin. The typo is that n = 385 and not n = 611.
- Lecture 3 and HapMap paper are posted!
- Updated the HW0 PDF with the following small fixes:
- In problem 2, assume that Hillary rolls her dice first.
- In problem 4a, being uniformly distributed means given a linkage, it has an equal chance of being in any of the 611 bins.
- Problem 4 should use the pbinom function not the pnorm function
4/8/2008
- We have added a link to the courseweb forums. You should be able to view the forum regardless of whether or not you are signed up for the course but you can only post to it if you are signed up. Please direct future homework and paper questions to the forums as that will be easier for us to get the information out to other students. Thanks!
4/12/2008
- Homework 0 was due yesterday but there are only 5 electronic submissions. Please submit your assignment as soon as possible. Also, there are quite a few of you in the class, to make things easier for us, please name your assignments in the following format:
HW#_LASTNAME.[DOC|PDF|TXT|SNW]
If you decide to fix your assignment, you are free to resubmit and just add the word "FIXED" or "NEW" or whatever so that we know which one to grade. Thanks. Solutions will be posted by Monday at which time we will not be accepting submissions.
4/14/2008
- Solution for homework 0 is posted.
4/15/2008
- Homework 1 posted.
4/17/2008
- We have a submission link for homework and project proposal submission.
http://diego.cs.ucla.edu/cs124/index.php/Submit
4/18/2008
Association study paper is posted!
4/20/2008
A note about accessing papers when you are not on campus. Please refer to the UCLA library proxy site about how to redirect your web browser to access the proxy script first. You will then be able to access the papers:
4/21/2008
We now have our Course Project Page : http://cs124project.wikidot.com
To become a member of Course Project Page, you will need a secret password. password : cs124_2008
4/21/2008
- Lecture 7 has been posted!
4/27/2008
- Lecture 8 has been posted!
- Getting relatedness information from the HapMap :
For those of you interested in getting relatedness information from the HapMap, it is available at: http://www.hapmap.org/downloads/samples_individuals/
Here are the first three lines of the CEU file in that directory: 1420 9 0 0 1 urn:lsid:dcc.hapmap.org:Sample:NA12003:1 1420 10 0 0 2 urn:lsid:dcc.hapmap.org:Sample:NA12004:1 1420 1 9 10 1 urn:lsid:dcc.hapmap.org:Sample:NA10838:1
I took out one column from the output to make it fit in the email.
The format is as follows. The first number is the "family ID". Within each family, the next three numbers are how the individuals are related. The first number is the individuals number. The next two numbers are the parent individual numbers. A 0 means that there is no parent in the data. So the first row is individual number 9 and the parents of that individual are not in the dataset. The third row is for individual number 1 and the parents of number 1 are number 9 (the first row) and number 10 (the second row).
The last column tells you the ID number of the sample as it is listed in the HapMap data.
If you notice that files is ordered so that each three rows is two parents followed by their child. You can use this to get the data more easily. If you take every third row, you get all of the children. If you skip every third row, you get the parents. For a lot of analyses, you should only take the parents which means you should skip every third row. This is because the child chromosomes are already in the sample since they are in the sample (remember the intro to human genetics).
You will notice that only the CEU and YRI populations have related individuals. The CHB and JPT are unrelated individuals.
4/29/2008
- Solution 1 has been posed.
- Homework 2 posted.
