run_scan1: Run scan1

In rqtl/qtl2cl: Command-Line Interface for R/qtl2

Run scan1

Description

Read in a bunch of data and then run qtl2::scan1().

Usage

run_scan1(
  genoprobs_file,
  pheno_file,
  output_file = NULL,
  map_file = NULL,
  kinship_file = NULL,
  addcovar_file = NULL,
  Xcovar_file = NULL,
  intcovar_file = NULL,
  weights_file = NULL,
  reml = TRUE,
  cores = 1,
  compress = FALSE
)

Arguments

genoprobs_file	Name of file with genotype probabilities
pheno_file	Name of file with phenotypes
output_file	Optional output RDS file. If NULL, print output as a table.
map_file	Optional (RDS) file containing map. Needed if output_file is NULL.
kinship_file	Optional file containing kinship matrix
addcovar_file	Optional file containing additive covariates
Xcovar_file	Optional file containing X chromosome covariates
intcovar_file	Optional file containing interactive covariates
weights_file	Optional file containing covariates
reml	If TRUE, use REML; otherwise, use maximum likelihood
cores	Number of CPU cores to use
compress	If TRUE, save a compressed RDS file (smaller but slower).

rqtl/qtl2cl documentation built on Oct. 13, 2024, 1:11 a.m.