pQTL Mediation analysis

Description Usage Arguments See Also Examples

For a given QTL haplotype probabilities qtl.geno and target target, the function sequentially tries to add each column m of mediator matrix as a covariate and calculates LOD statistic. The low LOD value indicates qtl.geno and target are conditionally independent given m, i.e. m is a mediator of causal relationship from qtl.geno to target.

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mediation.scan(target, mediator, annotation, qtl.geno, covar = NULL,
  method = c("double-lod-diff", "ignore", "lod-diff", "lod-ratio"),
  verbose = TRUE)

`target`	A numeric vector with gene/protein expression
`mediator`	A matrix, each column is one gene/protein's expression
`annotation`	A data frame with mediators' annotation, must include columns "chr" and "pos"
`qtl.geno`	A matrix, haplotype probabilities at QTL we try to mediate
`covar`	A matrix with additive covariates
`method`	A method to handle missing cases
`verbose`	If TRUE display information about the progress

plot.mediation, kplot

data(Tmem68)
med <- mediation.scan(target = Tmem68$target,
                      mediator = Tmem68$mediator,
                      annotation = Tmem68$annotation,
                      covar = Tmem68$covar,
                      qtl.geno = Tmem68$qtl.geno,
                      method = "double-lod-diff")
plot(med)