angelovici-lab/happi.gwas

A genome-wide association study (GWAS) tool written in R

happi.gwas's Issues

HAPPI.GWAS results not the same as GAPIT3

Hi,

I've run FarmCPU using the demo data provided using the command below, and run the same analysis using GAPIT within R, matching the same options as the Demo_FarmCPU.yaml file. Though the results are similar, there are in fact some differences.

Using HAPPI GWAS:
Rscript HAPPI_GWAS.R -GAPIT Demo_FarmCPU.yaml

Within R:
library(GAPIT3)
phenos = read.table("mdp_traits.txt", header = TRUE)
myGAPIT <- GAPIT(
Y=phenos,
Model.selection = TRUE,
model=c("FarmCPU"),
SNP.MAF = 0.05,
ncpus = 20,
file.G="mdp_genotype_chr",
file.Ext.G="hmp.txt",
file.from=1,
file.to=10,
file.path="./Demo/"
)

Is there a reason for differences in results if presumably the same model should be being fit?

Thank you,
Jonas