Software Packages



EMIM


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

References:

  • 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
  • Howey R and Cordell HJ (2012) PREMIM and EMIM: Tools for estimation of maternal, imprinting and interaction effects using multinomial modelling. BMC Bioinformatics 13(1):149
  • Howey R, Mamasoula C, Töpf A, Nudel R, Goodship JA, Keavney BD and Cordell HJ (2015) Increased power for detection of parent-of-origin effects via the use of haplotype estimation. Am J Hum Genet 97(3):419-434



  • Joint Effects Test


    Software implementing the Joint Effects (JE) interaction test can be found in the CASSI package.

    Reference:

  • Ueki M and Cordell HJ (2012) Improved statistics for genome-wide interaction analysis. PLoS Genet 8(4):e1002625



  • 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.