image: High-powered detection of genetic effects on DNA methylation...

In fanyue322/IMAGE: Title: High-Powered Detection of Genetic Effects on DNA Methylation Using Integrated Methylation QTL Mapping and Allele-Specific Analysis

Description

mQTL mapping in bisulfite sequencing studies by fitting a binomial mixed model, incorporating allelic-specific methylation pattern.

Usage

image(geno, data, K, Covariates = NULL, numCore = 1,
  fit.maxiter = 500, fit.tol = 1e-05, verbose = TRUE, pmt = 0)

Arguments

geno	a data list containing the genotype data.
data	a data list containing the methylation data.
K	a known kinship matrix. This matrix should be a positive semi-definite matrix with dimensions equal to the samplie size.
Covariates	a matrix containing the covariates subject to adjustment (Default = NULL).
numCore	a positive integer specifying the number of cores for parallel computing (default = 1).
fit.maxiter	a positive integer specifying the maximum number of iterations when fitting the generalized linear mixed model (default = 500).
fit.tol	a positive number specifying tolerance, the difference threshold for parameter estimates below which iterations should be stopped (default = 1e-5).
verbose	a logical switch for printing detailed information (parameter estimates in each iteration) for testing and debugging purpose (default = TRUE).
pmt	an integer specifying the permutation approach, set pmt equals either 1 or 2 will produce permuted p-values(default pmt=0).

Details

IMAGE properly accounts for the count nature of bisulfite sequencing data and incorporates allele-specific methylation patterns from heterozygous individuals to enable more powerful mQTL discovery. Binomial mixed models (BMM) are fitted using the penalized quasi-likelihood (PQL) method proposed by Breslow and Clayton (1993).

Value

loc	ordinal number of SNP-CpG pair being analyzed
numIDV	number of observations of SNP-CpG pair being analyzed
beta	the fixed effect parameter estimate for the predictor of interest.
se_beta	the standard deviation of fixed effect.
pvalue	P value for the fixed effect, based on the wald test.
h2	heritability of the transformed rate.
sigma2	total variance component.
converged	a logical indicator for convergence.

Author(s)

Yue Fan, Shiquan Sun, Xiang Zhou

References

Breslow, N.E. and Clayton, D.G. (1993) Approximate Inference in Generalized Linear Mixed Models. Journal of the American Statistical Association 88, 9-25.

Examples

data(exampledata)
attach(exampledata)
res=image(geno,data,K)
closeAllConnections()
detach(exampledata)

fanyue322/IMAGE documentation built on Jan. 30, 2020, 1:50 p.m.