methylqtl: Methylation quantitative trait locus mapping assisted with...

In 3211895/MethylQTL: What the Package Does Using Title Case

Description

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

Usage

MethylQTL <- function(geno,data,K,Covariates=NULL,numCore=1,fit.maxiter=500,fit.tol=1e-5,verbose=TRUE)

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.maxiter	a positive number specifying tolerance, the difference threshold for parameter estimates below which iterations should be stopped (default = 1e-5).

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.

Examples

data(ExampleData)
res=methylqtl(geno,data,K)

3211895/MethylQTL documentation built on May 21, 2019, 6:45 a.m.