mediation_qtl2: Test mediation across set of indexed drivers for 'qtl2' data

In fboehm/qtl2mediate: eQTl/pQTL Mediation analysis

Description

Test mediation across set of indexed drivers for 'qtl2' data

Usage

## S3 method for class 'listof_mediation_qtl2'
plot(x, ...)

## S3 method for class 'listof_mediation_qtl2'
autoplot(x, ...)

ggplot_listof_mediation_qtl2(x, plot_type = c("all", "causal",
  "reactive", "independent", "undecided"), minpvalue = 0.05,
  id_name = "mediator_id", ...)

mediation_qtl2(target, mediator, annotation, covar_tar, covar_med, kinship,
  genoprobs, map, drop_lod = 1.5, min_lod = 3, query_variant,
  cores = 1, target_scan, ...)

## S3 method for class 'mediation_qtl2'
plot(x, ...)

## S3 method for class 'mediation_qtl2'
autoplot(x, ...)

ggplot_mediation_qtl2(x, response = c("pvalue", "IC"),
  pattern_name = "pattern", ...)

Arguments

...	additional parameters for [mediation_index()]
target	vector or 1-column matrix with target values
mediator	vector or 1-column matrix with mediator values
annotation	optional annotation data frame for mediators
covar_tar	optional covariates for target
covar_med	optional covariates for mediator
kinship	optional kinship matrix among individuals
map	list of map positions
drop_lod	drop in 'LOD' (= 'LR/log(10)') to define index set
query_variant	function to query variant database
cores	number of cores to use
target_scan	optional object from [qtl2::scan1snps()] for target (created if missing)
genoprob	genoprob object of class [qtl2::calc_genoprob()]

Value

Object of class 'mediation_qtl2', which inherits from class [mediation_index()]

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