run_pylmm_exec: Run pyLMM for each phenotype and combine using metaSOFT

In TheJacksonLaboratory/mousegwas: Run in-bred mouse GWAS

Description

Run pyLMM for each phenotype and combine using metaSOFT

Usage

run_pylmm_exec(
  pylmm,
  geno_sfile,
  annot,
  phenofile,
  ksfile,
  nphen,
  output_head,
  metasoft_args = ""
)

Arguments

pylmm	pylmmGWAS.py executable
geno_sfile	the genotypes file
annot	SNP names in the same order in geno_sfile. Names will be replaced in the output file
phenofile	the phenotypes file
ksfile	kinship matrix file
nphen	number of phenotypes
output_head	Name of output files prefix

Value

The combined output file

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