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Linear mixed models (@lme4) + custom covariances + restrictions on model parameters
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R Merge branch 'master' of https://github.com/variani/lme4qtl Feb 14, 2019
data source code is public Jul 31, 2017
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inst trying bivar model Jan 2, 2019
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DESCRIPTION
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README.md added citation & ref. to article Mar 10, 2018

README.md

About lme4qtl

travis-ci build status

lme4qtl extends the lme4 R package for quantitative trait locus (qtl) mapping. It is all about the covariance structure of random effects. lme4qtl supports user-defined matrices for that, e.g. kinship or IBDs.

See slides bit.ly/1UiTZvQ introducing the lme4qtl R package or read our article / preprint.

Package Continuous response
stats lm(myTrait ~ myCovariate, myData)
lme4 lmer(myTrait ~ myCovariate + (1|myID), myData)
lme4qtl relmatLmer(myTrait ~ myCovariate + (1|myID), myData, relmat = list(myID = myMatrix))
Package Binary response
stats glm(myStatus ~ 1, myData, family = binomial)
lme4 glmer(myStatus ~ (1|myID), myData, family = binomial)
lme4qtl relmatGlmer(myStatus ~ (1|myID), myData, relmat = list(myID = myMatrix), family = binomial)

Note that rownames/colnames of myMatrix have to be values of myID variable, so matching between relationship matrix and grouping variable is possible. The order doesn't matter.

Quick start

library(lme4) # needed for `VarCorr` function
library(lme4qtl)

# load synthetic data set `dat40` distributed within `lme4qtl`
# - table of phenotypes `dat40`
# - the double kinship matrix `kin2`
data(dat40)

# (1) model continiuous trait `trait1`
mod <- relmatLmer(trait1 ~ AGE + SEX + (1|FAMID) + (1|ID), dat40, relmat = list(ID = kin2))

# get the estimation of h2
(vf <- as.data.frame(VarCorr(mod))[, c("grp", "vcov")])
#       grp      vcov
#1       ID 5.2845001
#2    FAMID 0.0000000
#3 Residual 0.6172059

prop <- with(vf, vcov / sum(vcov))

(h2 <- prop[1]) 
#[1] `0.895419`

# (2) model binary trait `trait1bin`
gmod <- relmatGlmer(trait1bin ~ (1|ID), dat40, relmat = list(ID = kin2), family = binomial)

Installation

# install.packages("devtools")
library(devtools)
install_github("variani/lme4qtl")

Citation

To cite the lme4qtl package in publications use:

  Ziyatdinov et al., lme4qtl: linear mixed models with flexible
  covariance structure for genetic studies of related individuals, 
  BMC Bioinformatics (2018)

Contact

You are welcome to submit suggestions and bug-reports at https://github.com/variani/lme4qtl/issues.

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