probTDT {trio} | R Documentation |
Computes the genotypic TDT for a a matrix representing SNP genotype probabilities.
probTDT(mat.geno, model = c("additive", "dominant", "recessive"), size = 50)
mat.geno |
a numeric matrix with one row for each SNP and 9 * t columns representing genotype probabilities for t trios. Each of the t
blocks (i.e. |
model |
type of model that should be fitted. Abbreviations are allowed. Thus, e.g., |
size |
the number of SNPs considered simultaneously when computing the parameter estimates. Ignored if |
... |
ignored. |
An object of class colTDT
consisting of the following numeric values or vectors, respectively:
coef |
the estimated parameter, |
se |
the estimated standard deviation of the parameter estimate, |
stat |
Wald statistic, |
RR |
the relative risk, i.e.\ for trio data, |
lowerRR |
the lower bound of the 95% confidence interval for |
upperRR |
the upper bound of the 95% confidence interval for |
usedTrios |
the number of trios affecting the parameter estimation, |
pMendelErr |
the sum across families of probabilities of Mendelian errors, |
... |
further internal parameters |
Margaret Taub, mtaub@jhsph.edu
Schaid, D.J. (1996). General Score Tests for Associations of Genetic Markers with Disease Using Cases and Their Parents. Genetic Epidemiology, 13, 423-449.
Schwender, H., Taub, M.A., Beaty, T.H., Marazita, M.L., and Ruczinski, I. (2011). Rapid Testing of SNPs and Gene-Environment Interactions in Case-Parent Trio Data Based on Exact Analytic Parameter Estimation. Biometrics, 68, 766-773.
Taub M.A., Schwender H., Beatty T.H., Louis T.A., Ruczinski I. (2012). Incorporating genotype uncertainties into the genotypic TDT for main effects and gene-environment interactions. Genetic Epidemiology, 36, 225-234.
# Load the simulated data. data(trio.data) # All SNPs in prob.mat.test can be tested by prob.tdt.out <- probTDT(prob.mat.test) # By default, an additive mode of inheritance is considered. # If another mode, e.g., the dominant mode, should be # considered, then this can be done by prob.tdt.out2 <- probTDT(prob.mat.test, model = "dominant") # By default, statistics for the top 5 SNPs are displayed. # If another number of SNPs, say 10, should be displayed, # then this can be done by print(prob.tdt.out2, top = 10) # The statistics for all SNPs (not ordered by their # significance) can be obtained by print(prob.tdt.out2, top = 0)