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
Software for generating case/pseudocontrol datasets for family-based association analysis
can be found in the PseudoCons 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.
