mediation_joint: Fit joint likelihood for 'target' and 'mediator' given...

In fboehm/qtl2mediate: eQTl/pQTL Mediation analysis

Description

Fit joint likelihood for 'target' and 'mediator' given 'driver'.

Usage

mediation_joint(target, mediator, driver, annotation, covar_tar = NULL,
  covar_med = NULL, kinship = NULL, driver_med = NULL,
  intcovar = NULL, fitFunction = fitQtl2, index_name = "pos", ...)

## S3 method for class 'mediation_joint'
plot(x, ...)

## S3 method for class 'mediation_joint'
autoplot(x, ...)

ggplot_mediation_joint(x, lod = TRUE, xlab = index_name,
  ylab = ylab_name, ...)

Arguments

target	vector or 1-column matrix with target values
mediator	matrix of mediators
driver	vector or matrix with driver values
annotation	A data frame with mediators' annotation with columns for 'facet_name' and 'index_name'
covar_tar	optional covariates for target
covar_med	optional covariates for mediator
kinship	optional kinship matrix among individuals
driver_med	optional driver matrix for mediators
intcovar	optional interactive covariates (assumed same for 'mediator' and 'target')
fitFunction	function to fit models with driver, target and mediator
index_name	name of index column (default 'pos')
...	additional parameters
test	Type of CMST test.

Value

Data frame with 'id' and 'LR' as well as 'annotation' columns.

Examples

data(Tmem68)
 
target <- Tmem68$target

# Reconstruct 8-allele genotype probabilities.
driver <- cbind(A = 1 - apply(Tmem68$qtl.geno, 1, sum), Tmem68$qtl.geno)
rownames(driver) <- rownames(Tmem68$qtl.geno)

# Find mediators with significant effect
med_lod <- mediator_lod(mediator = Tmem68$mediator,
                        driver = driver,
                        annotation = Tmem68$annotation,
                        covar_med = Tmem68$covar)
med_signif <- med_lod$id[med_lod$lod >= 5]
# Add info column.
med_lod$info <- paste("chr =", med_lod$chr)

med_joint <- mediation_joint(target = target,
                      mediator = Tmem68$mediator[, med_signif, drop = FALSE],
                      driver = driver,
                      annotation = med_lod,
                      covar_tar = Tmem68$covar,
                      covar_med = Tmem68$covar)
plot(med_joint)

fboehm/qtl2mediate documentation built on June 18, 2019, 8:27 p.m.