学习笔记--GWAS

进行GWAS：提取出合格的样本和SNP后，使用plink进行GWAS分析

输入文件：
1、 test.ped

The PED file is a white-space (space or tab) delimited file: the first six columns are mandatory:

 Family ID
 Individual ID
 Paternal ID
 Maternal ID
 Sex (1=male; 2=female; other=unknown)
 Phenotype

2、test.map

each line of the MAP file describes a single marker and must contain exactly 4 columns:

 chromosome (1-22, X, Y or 0 if unplaced)

 rs# or snp identifier

 Genetic distance (morgans)

 Base-pair position (bp units)

1. 将整理好的输入文件放入plink工作路径下

2. cmd进入plink工作目录（dir可查看目录信息）

3. 在plink目录运行：plink.exe --ped test.ped --map test.map --maf 0.05 --assoc
   

4. 在工作路径可查看结果文件：plink.assoc
   
   整理数据—gwasResults.txt
   

结果展示：

1、曼哈顿图

2、QQ图：

#install.packages("qqman")

library(qqman)
setwd("D:/Software/R/projects/GWAS")
pdf(file = 'manhattan.pdf', width=15)
rt=read.table("gwasResults.txt",header=T)
manhattan(rt, chr="CHR", bp ="BP", p="P", snp="SNP", col=c("blue4", "orange3"), ylim = c(0, 10),suggestiveline = F, genomewideline = -log10(3e-06))#临界值=0.05/snp数
dev.off()

# `QQplot`
pdf(file = 'QQplot.pdf', width=13)
qq(rt$P)
dev.off()

SNP注释: http://wannovar.usc.edu/