run_rqtl: Run R/qtl

In kbroman/GNapi: Connection to the GeneNetwork API

Run R/qtl

Description

Perform a genome scan using R/qtl

Usage

run_rqtl(
  dataset,
  trait,
  method = c("hk", "ehk", "em", "imp", "mr", "mr-imp", "mr-argmax"),
  model = c("normal", "binary", "2part", "np"),
  n_perm = 0,
  control_marker = NULL,
  interval_mapping = FALSE,
  url = gnapi_url()
)

Arguments

dataset	ID for dataset being used (Short_Abbreviation)
trait	ID for trait being mapped
method	Indicates whether to use the EM algorithm, imputation, Haley-Knott regression, the extended Haley-Knott method, or marker regression.
model	The phenotype model: the usual normal model, a model for binary traits, a two-part model, or non-parametric analysis
n_perm	Number of permutations
control_marker	Name of marker to use as a covariate
interval_mapping	Whether to use interval mapping
url	The URL for the GeneNetwork API

Value

A data frame

Examples

out <- run_rqtl("HC_M2_0606_P", "1418701_at")

kbroman/GNapi documentation built on July 29, 2023, 10:10 a.m.