suzkami / gwas_hmp_to_plot

GWAS_hmp_to_plot

#require:

1 load function

source("https://raw.githubusercontent.com/suzkami/GWAS_hmp_to_plot/main/GWAS_RtoP_su.R")
source("https://raw.githubusercontent.com/suzkami/GWAS_hmp_to_plot/main/function_GWAS.R")

2 input:

(A)Genotype file (hapmap): df.hmp.txt
(B)Phenotype file (same accession ID as hapmap file) df.txt
(C)LD calculate by Plink or TASSEL; for candidate region narrow down.

note

!Only support the output formation from TASSEL and EMMAX.
!When use EMMAX, the out put prefix should be same as the Phenotype name.

#example GWAS(hmpfile = "./6xhmp50362**.hmp.txt**",
LDfile = "./GRDA6X50362**.ld**",
phenofile = "./Test.txt",
type = "MLM", ptype_filte = "./ptype.txt")

*Phenotype ID name sould be *EMMAX must use emmax-intel64