execute_lmm: Run lmm 2 (LRT) on the data with LOCO

In TheJacksonLaboratory/mousegwas: Run in-bred mouse GWAS

Description

Run lmm 2 (LRT) on the data with LOCO

Usage

execute_lmm(
  genotypes,
  phenotypes,
  annot,
  covars,
  basedir,
  groups = NULL,
  loco = TRUE,
  runmetasoft = FALSE,
  metasoft_args = ""
)

Arguments

genotypes	the genotypes data.table
phenotypes	the phenotypes data.table
annot	annotations of SNPs file
covars	covariates data.table
basedir	dir to write files to
groups	A list of vectors, each containing phenotypes indices to run as multivariate. The return file will be the first group unless runmetasoft is TRUE
loco	perform LOCO (default FALSE)
runmetasoft	Run metasoft. Return the output file.
metasoft_args	additional metasoft arguments
exec	gemma executable

Value

The unified output file

TheJacksonLaboratory/mousegwas documentation built on Sept. 27, 2021, 9:14 a.m.