mediation.scan.qr: Runs genome-wide mediation scan from a QR decomposition...

In gkeele/miqtl: Suite of QTL Mapping Functions

Runs genome-wide mediation scan from a QR decomposition object based on a specified QTL and phenotype data file.

Description

This function runs the genome scan based on a QR decomposition object and phenotype data file. This functionality only works for fixed effect models. Currently written for chromatin mediation of local-eQTL, though could easily be generalized to any pairing of mediator and outcome.

Usage

mediation.scan.qr(
  mediation.qr.object,
  data,
  phenotype,
  chr = "all",
  id = "SUBJECT.NAME",
  debug.single.fit = FALSE,
  use.progress.bar = TRUE,
  ...
)

Arguments

mediation.qr.object	Output object from extract.mediation.qr()
data	A data frame with outcome. Should also have IDs that link to IDs in the genome cache, often with the individual-level ID named "SUBJECT.NAME", though others can be specified with pheno.id.
phenotype	The column name (or function of column name) of a variable in data. This will become the outcome of the mediation scan.
chr	DEFAULT: "all". Specifies which chromosomes to scan.
id	DEFAULT: "SUBJECT.NAME". The is the individual-level ID that is associated with data points in the phenotype data. This should be unique for each data point.
debug.single.fit	DEFAULT: FALSE. If TRUE, a browser() call is activated after the first locus is fit. This option allows developers to more easily debug while still using the actual R package.
use.progress.bar	DEFAULT: TRUE. Results in a progress bar being displayed.

Examples

mediation.scan.qr()

gkeele/miqtl documentation built on Sept. 13, 2024, 5:49 a.m.