run.qr.permutation.threshold.mediation.expression.scans: Runs mediation permutation scans for significance thresholds...

In gkeele/miqtl: Suite of QTL Mapping Functions

Runs mediation permutation scans for significance thresholds based on an index permutation matrix object, the phenotype data, and pre-computed QR decompositions for all the models. Currently designed for mediation through gene expression.

Description

This function runs permutation scans in order to calculate significance thresholds for mediation analysis. Its results are most valid when done in a fixed effect model setting and observations are exchangeable.

Usage

run.qr.permutation.threshold.mediation.expression.scans(
  perm.ind.matrix,
  mediation.qr.object,
  genomecache,
  phenotype,
  data,
  gene.data,
  keep.full.scans = FALSE,
  scan.index = NULL,
  id = "SUBJECT.NAME",
  chr = "all",
  pos.is.bp = TRUE,
  use.progress.bar = TRUE,
  ...
)

Arguments

perm.ind.matrix	Output object from generate.qr.permutation.index.matrix().
mediation.qr.object	Output object from extract.mediation.expression.qr().
genomecache	The path to the genome cache directory. The genome cache is a particularly structured directory that stores the haplotype probabilities/dosages at each locus. It has an additive model subdirectory and a full model subdirectory. Each contains subdirectories for each chromosome, which then store .RData files for the probabilities/dosages of each locus.
phenotype	The column name (or function of column name) of a variable in data. This will become the outcome of the genome scan.
data	A data frame with outcome and potential covariates. 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 id.
keep.full.scans	DEFAULT: FALSE. If TRUE, all p-values are kept from all loci. If FALSE, only the minimum p-value is kept from each scan, greatly reducing size of output.
scan.index	DEFAULT: NULL. If NULL, all permutations are run. Integer vector can be specified to run just a subset of the permutations.
id	DEFAULT: "SUBJECT.NAME". This is the individual-level ID that is associated with data points in the phenotype data. This should be unique for each data point.
chr	DEFAULT: "all". Specifies which chromosomes to scan.
pos.is.bp	DEFAULT: TRUE. If the pos variable in data is bp, use the default. If it is Mb, then set to FALSE.
use.progress.bar	DEFAULT: FALSE. Results in a progress bar while code runs.

Examples

run.qr.permutation.threshold.mediation.expression.scans()

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