GWAS分析软件GAPIT学习笔记

1：只需要输入hmp格式的基因型文件与表型文件即可

2：软件安装

source("http://www.bioconductor.org/biocLite.R") 

biocLite("multtest") 

install.packages("gplots")
install.packages("LDheatmap")
install.packages("genetics")
install.packages(“EMMREML”)
install.packages("scatterplot3d") 

3：软件加载

library(multtest)
library(gplots)
library(LDheatmap)
library(genetics)
library(EMMREML)
library(compiler) 

source("http://zzlab.net/GAPIT/gapit_functions.txt") 

source("http://zzlab.net/GAPIT/emma.txt") 

myG<-read.table("/Users/apple/Desktop/GWAS_pipeline/mdp_genotype_test.hmp.txt",head=FALSE)

myY<-read.table("/Users/apple/Desktop/GWAS_pipeline/mdp_traits.txt",head=TRUE)

myGAPIT <-GAPIT(Y=myY,G=myG,

kinship.cluster=c("average","complete", "ward"),

kinship.group=c("Mean","Max"),

SNP.MAF=0,

SNP.FDR=1,

PCA.total=3,

Model.selection = TRUE)

备注：画出来的图不好看，不过有初步结果可以自己写脚本美观下。