gemma_lmm: Run LMM via GEMMA

In surh/HMVAR: Human Microbiome Variant Analysis in R

Description

Tested with GEMMA 0.93b modified by bugwas package.

Usage

gemma_lmm(
  geno_file,
  pheno_file,
  snp_file,
  kinship_file,
  cov_file = NULL,
  gemma = "gemma",
  outdir = "lmm/",
  maf = 0,
  prefix = "lmm"
)

Arguments

geno_file	Mean genotype file in BIMBAM format. See GEMMA manual for details.
pheno_file	Phenotype file in BIMBAM format. See GEMMA manual for details.
snp_file	SNP annotation file in BIMBAM format. See GEMMA manual for details.
kinship_file	Kinship file in GEMMA format. See GEMMA manual for details.
cov_file	Covariates file in BIMBAM format. See GEMMA manual for details.
gemma	GEMMA executable.
outdir	directory to write output.
maf	Minor allele frequency threshold for SNPs to test.
prefix	Prefix for output filenames.

References

http://www.xzlab.org/software/GEMMAmanual.pdf

surh/HMVAR documentation built on Aug. 18, 2021, 1:21 a.m.