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University of Nebraska–Lincoln

Department of Statistics

Turning data into knowledge to solve real world problems


Biom 896: Statistical Genomics

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Examples

SAS

  • IML program to calculate power for BC and F2 designs: IMLPower.sas
       Updated: 09/19/02 at 04:12:03 PM
  • IML program to calculate Information Content for a BC designs: icbc.sas
       Updated: 09/26/02 at 03:38:33 PM
  • c2, WLS, and LRT example: peas.sas
  • Power example: peapow.sas
  • Recombination
    MLE with Proc NLIN: f2recomb.sas
    A simple example of obtaining likelihood confidence intervals: simple_ci.sas
    Bootstrap mean and standard deviation: simple_boot.sas
  • Calculate 3 locus log likelihoods: 3locus_like.sas
  • Draw 10 bootstrap samples: boot.sas
  • Interval Mapping:
    Barley Marker data: barley.dat
    Barley Trait data: barley.traits
    Create SAS data set raw data: barley.sas
       Updated: 08/21/03 at 03:52:18 PM
    Barley data generated by QTL Cartographer: barley1.data
       Updated: 08/21/03 at 03:52:19 PM
    Create SAS data set from QTL Cartographer: barley1.sas
       Updated: 08/21/03 at 03:52:19 PM
    Least squares analysis program: DHnlin.sas
       Updated: 08/21/03 at 03:52:22 PM
    Interval mapping program: DHml.sas
       Updated: 08/21/03 at 03:52:21 PM
  • Composite Interval Mapping
    • Sample data set:
      • Map data: sample.map
           Updated: 10/08/02 at 02:58:10 PM
      • Cross data: sample.cro
           Updated: 10/08/02 at 02:58:07 PM
      • SAS program: sample.sas
           Updated: 10/08/02 at 11:55:36 AM
    • CIM analysis program: CIM.sas
         Updated: 08/21/03 at 03:52:20 PM
    • IM analysis program: IM.sas
         Updated: 12/04/02 at 01:25:04 PM
      includes both the L&K and Perm. Thersholds
  • Random QTL effect
    • Daughter Design:
      • Daughter Design data: sire.dat
           Updated: 10/29/02 at 12:12:10 PM
      • Mixed Analysis: sire.sas
           Updated: 10/29/02 at 12:12:07 PM
    • General Pedigree:
      • Gametic Covariance Matrix: Mcalc.sas
           Updated: 11/06/02 at 09:30:19 AM
    • QTL REML analysis:
      • Program: QTLREML.sas
           Updated: 11/18/02 at 10:41:16 AM
      • Data file: datafile1q
           Updated: 08/21/03 at 03:52:21 PM
      • Pedigree: pedfile
           Updated: 11/18/02 at 10:41:09 AM
      • Marker data: pdq.input1
           Updated: 11/18/02 at 10:40:56 AM
  • Power and Sample Size determination
    • Backcross Power analysis Power.sas
         Updated: 12/09/02 at 01:53:00 PM
    • Daughter Design Power analysis Power_HS.sas
         Updated: 12/09/02 at 01:49:39 PM

Steve Kachman <skachman@unl.edu>
Last modified: Wed Feb 20 2008