| ll {TRD} | R Documentation |
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' |
Details
If the following warning messages occur, increase the population and sample size. Warning messages: glm.fit: fitted rates numerically 0 occurred
Value
Summary table |
Summary statistics of fitting the loglinear model |
Author(s)
Lam Opal Huang
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
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')