one.rGLM.test {rGLM} | R Documentation |
Return a likelihood ratio like test of haplotype effect based on rGLM approach
Description
This function returns a likelihood ratio like test of haplotype effect comparing two nested models fit with rGLM function.
Usage
one.rGLM.test(nonSNPcolumns,hypoDat, family=binomial, allelic=TRUE, pooling.tol = 0.05, maxit=200, tol=0.001, lambda=0, trace=FALSE)
Arguments
nonSNPcolumns |
number of columns that do not contain genotype information in hypoDat data set |
hypoDat |
data set that contains the response variable and genotypes on SNPs |
family |
binomial, poisson, gaussian or freq are supported, default=binomial |
allelic |
TRUE if single-locus SNP genotypes are in allelic format and FALSE if in genotypic format; default is TRUE. |
pooling.tol |
pooling tolerance; by default set to 0.05 |
maxit |
maximum number of iterations of the EM algorithm; default=50 |
tol |
convergence tolerance in terms of either the maximum difference in parameter estimates between iterations or the maximum relative difference in parameter estimates between iterations, which ever is larger. Default is 0.001. |
lambda |
tuning parameter lambda |
trace |
indicates whether or not some internal results should be printed; default is FALSE. |
Value
data |
data set used in the association test |
pre.hapassoc.data |
data list obtained from pre.hapassoc function |
LRTstat |
an likelihood ratio like statistic |
regrH1 |
a list obtained from rGLM function based on the alternative hypothesis, i.e., a full model is used in the regression |
regrH0 |
a list obtained from rGLM function based on the null hypothesis, i.e., a formula as "affected~1." is used in the regression |
H1.converged |
indicate if regrH1 is converged |
H0.converged |
indicate if regrH0 is converged |
na.resason |
indicate if LRTstat exists and reason that LRTstat is unavailable; If LRTstat exists, the value is "conv", while the values are "na.pre.hapassoc", "unconv.H1", "unconv.H0", "unconv.H1.H0" when LRTstat is unavailable due to prepare the data list by pre.hapassoc function, H1.converged=FALSE, H0.converged=FALSE, and H1.converged=H0.converged=FALSE, respectively. |
lambda |
tuning parameter |
References
Guo W, Lin S. 2008. Generalized linear modeling with regularization for detecting
common disease rare haplotype association.
[Package
rGLM version 2.0
Index]