TRD (version 1.1)

ll: Fit Loglinear model with and without adjustment for TRD.

Description

Use input data, either sample of case-trios ('sample') or count data for 15/16-MFC-genotype categories ('counts') to fit loglinear model with (Model 2) and without (Model 1) adjustment for TRD, model type could be genotype relative risk ('grr'), dominant ('dom'), gene-dosage ('gd'), genotype relative risk with imprinting variable ('grri'), dominant with imprinting variable ('domi'), or gene-dosage with imprinting variable ('gdi'). Note that the models fit only complete trios with no missing data.

Usage

ll(data, data.type, tmother, tfather, model.type)

Arguments

data

input data can be (1) case- and/or control-trios dataset with first column as disease status (1=case, 0=control), the second, third and forth columns as maternal, paternal and child genotypes. The fifth column, if entered as part of the input data, is the parent-of-origin indicator of disease allele in a heterozygous child (a value of 1 indicates the mother transmitted the disease allele and 0 indicates the father transmitted). The parent-of-origin indicator is only meaningful for a heterozygous child. (2) a count dataset for the 15 or 16-MFC-genotype categories obtainable from the function strata.cnt(..), with the latter having 2 categories (111M & 111F) for triply heterozygous trios.

data.type

type of data: 'sample' or 'counts'

tmother

transmission ratio of minor alleles from mother to child

tfather

transmission ratio of minor alleles from father to child

model.type

'grr', 'dom', 'gd', 'grri', 'domi', or 'gdi'

Value

Summary table

Summary statistics of fitting the loglinear model

Details

If the following warning messages occur, increase the population and sample size. Warning messages: glm.fit: fitted rates numerically 0 occurred

References

Huang LO, Infante-Rivard C, Labbe A, (2015). Modeling sex-of-parent-specific Transmission Ratio Distortion and imprinting effect in loglinear model using case-trios.(Working manuscript)

Huang LO, Infante-Rivard C, Labbe A, (2015). Adjustment for Transmission Ratio Distortion in the analysis of case-parent trios using a loglinear model.(Working manuscript)

Weinberg CR, Wilcox AJ, Lie RT (1998) A log-linear approach to case-parent-triad data: assessing effects of disease genes that act either directly or through maternal effects and that may be subject to parental imprinting. American Journal of Human Genetics 62: 969-78.

See Also

rtrios strata.cnt

Examples

trios=rtrios(100000,500,0.1,0.2,0.3,1,0.5,0.5,0.1)
out=ll(trios$case,'sample',0.5,0.5,'grr')

cnt=strata.cnt(trios$case)
out=ll(cnt,'counts',0.5,0.5,'grr')