scan.qr: Runs genome scan from a QR decomposition object and phenotype...

In gkeele/miqtl: Suite of QTL Mapping Functions

Runs genome scan from a QR decomposition object 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.

Usage

scan.qr(
  qr.object,
  data,
  phenotype,
  return.allele.effects = FALSE,
  chr = "all",
  id = "SUBJECT.NAME",
  just.these.loci = NULL,
  debug.single.fit = FALSE,
  use.progress.bar = TRUE,
  ...
)

Arguments

qr.object	QR decomposition output from extract.qr().
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.
phenotype	The column name (or function of column name) of a variable in data. This will become the outcome of the genome scan.
return.allele.effects	DEFAULT: FALSE. If TRUE, allele effects, fit as fixed effects, are returned as a matrix.
chr	DEFAULT: "all". Specifies which chromosomes to scan.
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.
just.these.loci	DEFAULT: NULL. Specifies a reduced set of loci to fit. If loci is just one locus, the alternative model fit will also be output as fit1.
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 while code runs.

Examples

scan.qr()

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