精神分裂症GWAS

背景

可在这里申请下载数据。

参考文献PMID25056061

使用qqman包进行曼哈顿图等可视化分析。

安装R包

install.packages("qqman")

载入与初始化

library("qqman")

# 读入
SCZ <- read.table('rall.txt', header=TRUE, sep="\t")
# 由于曼哈顿图需要的CHR变量是数字(int)，所以需要先把原始文件里的hg19chrc这一列改造一下
# 如把chr1改成1，把chrX改成23
# 去掉chr
SCZ$hg19chrc <- gsub("chr", "", SCZ$hg19chrc)
# 将X改成23
SCZ$hg19chrc <- gsub("X", "23", SCZ$hg19chrc)
# 把hg19chrc这一列的类型改成int
SCZ$hg19chrc <- as.integer(SCZ$hg19chrc)

# 大概是需要一条准线
genomeWideLine = 0.05 / nrow(SCZ)

画图

# 画曼哈顿图
manhattan(SCZ, chrlabs=c(1:22, "X"), genomewideline=-log10(genomeWideLine),
    chr = "hg19chrc", bp = "bp", p = "p", snp = "snpid",
    suggestiveline=FALSE, main="PGC SCZ GWAS")

SCZ

输出最明显的那个染色体

# 说要输出最明显的那个染色体，明显是6号咯
manhattan(subset(SCZ, CHR==6), genomewideline=-log10(genomeWideLine),
    chr = "hg19chrc", bp = "bp", p = "p", snp = "snpid",
    suggestiveline=FALSE, main="PGC SCZ GWAS chr6")

SCZ_chr6

最明显的点标出来

# 根据图把最明显的那个点也可视化出来
# rs115329265
manhattan(subset(SCZ, CHR==6), genomewideline=-log10(genomeWideLine),
    chr = "hg19chrc", bp = "bp", p = "p", snp = "snpid",
    suggestiveline=FALSE, main="Most Significant Locus",
    annotatePval=1e-30, annotateTop=TRUE)