mediation.scan: Mediation Scan.
In churchill-lab/qtl2api: QTL2 API Library

mediation.scan

R Documentation

Mediation Scan.

Description

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.

Usage

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

Arguments

`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