Assignments for Human Genetics II: Introductory Statistical Genetics

Assignments for Human Genetics II: Introductory Statistical Genetics

Current Assignments:

Final Exam. Due 03.21.03 (Friday) at 12:00 pm. You can download a copy here Friday after section (11:00 am). Please submit them electronically to bvoight@uchicago.edu or deliver a hard copy to CLSC 505h (Ben’s office) by Thursday at 5:00 pm.

Nancy will be out of town starting the 19^th, so if you have any questions for her, make sure you catch her before then. I will be available the whole week, and will still hold my office hours as usual, if you want to come and find me. Otherwise, email me to make an appointment if you have questions or issues.

Previous Assignments:

Problem Set Four: Due 03.14.03 at 5:00 pm. [Download]

You can download the files you will need to do the analysis using the following (please note whitespaces):

cp /rusr/nancy/forclass/run.me.class307 .

cp /rusr/nancy/forclass/chromo2.map.class307 .

cp /rusr/nancy/forclass/chromo2.data.class307 .

cp /rusr/nancy/forclass/19.typed.weights.dat .

cp /rusr/nancy/forclass/19.11.weights.dat .

cp /rusr/nancy/forclass/19.12.weights.dat .

cp /rusr/nancy/forclass/19.22.weights.dat .

cp /rusr/nancy/forclass/tally.x .

You can obtain asm.solaris now using the following command:

cp /rusr/nancy/asm.solaris .

Problem Set Three: Due 02.28.03 at 5:00 pm (via email), or hard copies before 12:00 noon please! [Download]

You can download the files you will need to do for the analysis using the following (please note whitespaces):

cp /rusr/nancy/forclass/chromo21.bmi .
cp /rusr/nancy/forclass/chromo21.bmi.datain.dat .
cp /rusr/nancy/forclass/run.me.vc.21 .

The above run.me file does not include information regarding the ps option. If you want to look at a sample run.me file that would output postscript files of the NPL, LOD, information content as well as variance component ps files, you can look here.

Midterm on 02.11.03 handed out at 9:00 AM. Due 02.18.03 at 9:00 AM [DOC]

To complete the midterm, you will need to access some files from Nancy's computer into your account. The files are located in /rusr/nancy/, and there will be six files you need. Thus, use the following lines (while logged in as your stud ID username) in UNIX to acquire the files. Please note the whitespace between the .data and .marker and the ".":

For problem 2:
cp /rusr/nancy/dumb1.data .
cp /rusr/nancy/dumb2.data .
cp /rusr/nancy/dumb3.data .
cp /rusr/nancy/dumb.markers .

For problem 3:
cp /rusr/nancy/dumber.data .
cp /rusr/nancy/dumber.markers .

Email me (Ben) at bvoight@uchicago.edu if you have any problems with this, be sure to include your username and password and I'll make sure you can get at the files, but the above ought to work.

Other Comments:
1. For question 3c, where you are asked to construct a model for the DUMBER locus, assume that it has the same prevalence as DUMB (which is .01).

Problem Set Two. Due 01.31.03 at 5:00 pm. [Download] [Answer Key]

Note: You can copy the required tdt file (Ghunt.11.for.tdt) into your student account using the following command:

cp /rusr/nancy/forclass/Ghunt.11.for.tdt .

Most student accounts now have this file, but if you lose or misplace it (or whatever) you can recopy it. And the 11final.ped file you ought to already have in your student account from the last homework assignment.

Problem Set One: Due 01.24.03 at 5:00 pm. [Download]

Tips:
1. Use the photo command in Genehunter to save the output file rather than saving the entire scanned output to file. It saves space and time if you run analysis under different dmodels. Make sure you use different file names so that you don't overwrite a result!
2. Use the top command in UNIX to observe the number of students running analyses that you are. If more than 3 students are running things, try to run your items at another time/date.
3. Included are some sample run.me files for you to use in genehunter. To speed up your analyses, use this command in UNIX:

gh < run.me > temp &

Assuming you have a file named run.me with the appropriate commands you want genehunter to implement. The command will send all the output genehunter makes to a file called temp. Make sure the run.me file contains the photo command. A sample run.me file might look something like:

load Ghunt.11.1.dom
haplotype off
score pairs
scan 11final.1
photo myresult.out
total
quit

Obviously, you will be looking at different marker (e.g. Ghunt.11) and pedigree (11final.ped) files, which will need to be changed in the above example.

4. Here are some sample pedigree and marker files for your reference. I used them as "toy" examples in section (01.17.03).

5. Also, you can refer to the section notes if you want to refer back to something we did in section (01.17.03).

Updated 03.13.03