run_pylmm: Run pylmm

In TheJacksonLaboratory/mousegwas: Run in-bred mouse GWAS

Description

Run pylmm

Usage

run_pylmm(
  genotypes,
  phenotypes,
  annot,
  covars,
  basedir,
  pylmm,
  pylmm_kinship,
  loco = TRUE,
  metasoft_args = ""
)

Arguments

genotypes	All genotypes as a data.table, including three columns of rs, major, minor
phenotypes	All phenotypes (n x p)
annot	SNPs annotations
covars	Covariates or null
basedir	wd
pylmm_kinship	pyLMMKinship executable
loco	Use LOCO or not
metasoft_args	additional arguments for metasoft
pymm	PyLMM executable

Value

the output file

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