Software and Teaching Material


Software Packages

EMIM

Software for Estimation of Maternal, Imprinting and interaction effects using Multinomial modelling can be found in the EMIM package.

Reference:

  • Ainsworth HF, Unwin J, Jamison DL and Cordell HJ (2011) Investigation of maternal effects, maternal-foetal interactions and parent-of-origin effects (imprinting), using mothers and their offspring. Genetic Epidemiology 35:19-45



    • Threelocarp

    Software for carrying out model-free linkage analysis of up to three linked or unlinked loci using affected relative pairs is available in the threelocarp package.

    References:

  • Cordell HJ, Wedig GC, Jacobs KB and Elston RC (2000) Multilocus linkage tests based on affected relative pairs. American Journal of Human Genetics 66: 1273-1286.
  • Cordell HJ, Todd JA, Bennett ST, Kawaguchi Y and Farrall M (1995) Two-locus maximum lod score analysis of a multifactorial trait: joint consideration of IDDM2 and IDDM4 with IDDM1 in type 1 diabetes. American Journal of Human Genetics 57: 920-934.



    • Case/pseudocontrol analysis

    David Clayton's software for generating case/pseudocontrol datasets for family-based association analysis.

    For Stata versions, see David Clayton's genassoc package

    For R versions see David Clayton's DGCgenetics package

    References:

  • Cordell HJ, Barratt BJ and Clayton DG (2004) Case/pseudocontrol analysis in genetic association studies: a unified framework for detection of genotype and haplotype associations, gene-gene and gene-environment interactions and parent-of-origin effects. Genetic Epidemiology 26:167-185.
  • Cordell HJ and Clayton DG (2002) A unified stepwise regression procedure for evaluating the relative effects of polymorphisms within a gene using case/control or family data: application to HLA in type 1 diabetes. American Journal of Human Genetics 70: 124-141.




    • Teaching Material


    Click here for exercises for the MRes Module MMB8014 (Genetics of Common Disease), Newcastle, November/December 2011.



    Click here for case/control exercises using PLINK, R (DGCgenetics library) and UNPHASED (running under linux).

    Click here for case/control exercises using R (DGCgenetics library) and Unphased (running under linux).

    Click here for family-based association exercise using UNPHASED (running under linux).

    Click here for family-based exercises using R (DGCgenetics library, running under linux).

    Click here for case/control and case-only exercises using R (running under linux).

    Click here for case/control exercises using Stata and R (running under linux).

    Click here for family-based association exercises using Stata and R (running under linux).



    Click here for exercises for the MSc in Medical Genetics, Newcastle, November 2008.

    Click here for exercises for the Rotterdam course in Model-free Analysis (GE05), March 2008.

    Click here for exercises for the MSc in Medical Genetics, Newcastle, Feb 8th 2008.

    Click here for exercises for the European School of Genetic Medicine: 3rd Course in Statistical Genetic Analysis of Complex Phenotypes, June 24th-27th 2007, Bertinoro di Romagna, Italy.

    Click here for exercises for the MSc in Medical Genetics, Newcastle, Feb 22nd 2007.

    Click here for exercises for the Workshop on Genetic Association Studies, Jan 24th-25th 2007, Shaheed Beheshti Medical University, Iran.

    Click here for exercises for the Wellcome Trust Advanced Course on Design and Analysis of Genetic-Based Association Studies, Oct 3rd-7th 2006, Hinxton, UK.

    Click here for exercises for the European School of Genetic Medicine, May 3rd-5th 2006, Bertinoro di Romagna, Italy.