calc_mediation: Calculate mediation scores between phenotype and gene...

In AndersenLab/linkagemapping: Functions for the Mapping of Andersen Lab RIAILs and RILs

Description

Calculate mediation scores between phenotype and gene expression

Usage

calc_mediation(peak, expression_probe, phenodf, cross, scaled = T, lm = FALSE)

Arguments

peak	peak marker of phenotype QTL in format chr:pos
phenodf	Dataframe for phenotype in the form of strain, trait, phenotype with the strain matching RIL from set1 (where we have expression data)
cross	Empty cross object, used to gather genotype information (does not need to be merged with phenotype, but can be)
scaled	Boolean noting if the phenotype should be scaled for a mean of 0 and standard devitaiton of 1. Default is TRUE
lm	Boolean argument. If TRUE, a set of linear models will be used to calculate mediation. If FALSE, mediation will be calculated from the R package "mediation"
probe	probeID from expression data

AndersenLab/linkagemapping documentation built on Jan. 27, 2022, 10:44 p.m.