加载中…使用R软件包LDheatmap绘制连锁不平衡热图
(2016-06-23 17:14:47) | 分类： R语言与数理统计 |
1:软件包安装
install.packages("LDheatmap")
library(LDheatmap)
2:运行例子：
data("CEUData")
数据“CEUData”包含两部分：基因型数据CEUSNP和SNP位点数据CEUDist
CEUSNP数据如下：
| rs4615512 | rs2283089 | rs1894731 | rs2283092 | rs2283093 | rs6978939 | rs6979287 | rs6979572 | rs2283094 | rs2283095 | rs6467111 | rs1111183 | rs2237789 | rs2299531 | rs2299532 |
| T/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/T | C/T | A/A | T/C | A/T |
| T/C | C/T | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/T | C/T | A/A | T/C | A/T |
| T/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/C | C/T | A/A | T/C | A/T |
| C/C | A/G | T/C | C/T | T/G | T/G | T/A | C/T | C/T | C/C | C/C | A/G | A/A | ||
| T/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/C | C/T | A/A | T/C | A/T |
| T/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/C | C/C | A/A | T/T | A/A |
| C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/T | C/T | A/A | T/C | A/T | |
| T/T | C/C | A/G | T/C | C/T | T/G | T/G | T/A | C/C | C/T | C/C | C/T | A/G | T/C | A/T |
| C/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | T/T | C/C | C/T | C/C | A/A | T/T | A/A |
| T/T | C/T | G/G | C/C | C/T | G/G | G/G | T/A | C/T | C/T | C/T | C/C | A/G | A/A | |
| T/T | C/C | A/G | T/C | C/T | T/G | T/G | T/A | C/C | C/T | C/C | C/T | A/G | A/T | |
| T/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/C | C/T | A/A | T/C | A/T |
| T/T | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/C | C/C | C/C | T/T | A/A | C/C | T/T |
| T/C | C/C | A/G | T/C | C/T | T/G | T/G | T/A | C/T | C/T | C/C | C/C | A/G | T/T | A/A |
| T/T | C/C | A/G | T/C | C/T | T/G | T/G | T/A | C/C | C/T | C/T | C/T | A/G | T/C | A/T |
| C/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | T/T | C/C | C/C | C/C | A/A | T/T | A/A |
| C/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | T/T | C/C | C/T | C/C | A/A | T/T | A/A |
| T/C | C/C | A/G | T/C | C/T | T/G | T/G | T/A | C/T | C/T | C/C | C/C | A/G | T/T | A/A |
| C/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | T/T | C/C | T/T | C/C | A/A | T/T | A/A |
| T/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/C | C/T | A/A | T/C | A/T |
| C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/C | C/C | C/C | T/T | A/A | T/T | ||
| T/T | C/T | A/G | T/C | C/C | T/G | T/G | T/T | C/T | C/C | C/T | C/T | A/A | T/C | A/T |
| T/C | T/T | A/G | T/C | C/C | T/G | T/G | T/T | T/T | C/C | T/T | C/C | A/A | T/T | A/A |
| T/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/C | C/C | A/A | T/T | A/A |
| T/T | C/C | A/G | T/C | C/T | T/G | T/G | T/A | C/C | C/T | C/C | C/T | A/G | T/C | A/T |
| T/T | C/C | A/G | T/C | C/T | T/G | T/G | T/A | C/C | C/T | C/C | C/T | A/G | T/C | A/T |
| T/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/C | C/T | A/A | T/C | A/T |
| T/T | C/C | G/G | C/C | T/T | G/G | G/G | A/A | C/C | T/T | C/C | C/C | G/G | T/T | A/A |
| C/T | A/G | T/C | C/T | T/G | T/G | T/A | C/T | C/T | C/T | C/C | A/G | A/A | ||
| T/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/T | C/T | A/A | T/C | A/T |
| T/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/C | C/T | A/A | T/C | A/T |
| C/C | C/T | A/A | T/T | C/C | T/T | T/T | T/T | T/T | C/C | C/T | C/C | A/A | T/T | A/A |
| T/T | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/C | C/C | C/C | T/T | A/A | C/C | T/T |
| T/C | C/C | A/G | T/C | C/T | T/G | T/G | T/A | C/T | C/T | C/T | C/C | A/G | T/T | A/A |
| T/T | C/C | A/G | T/C | C/T | T/G | T/G | T/A | C/C | C/T | C/C | C/T | A/G | T/C | A/T |
| T/T | C/C | G/G | C/C | T/T | G/G | G/G | A/A | C/C | T/T | C/C | C/C | G/G | T/T | A/A |
| T/T | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/C | C/C | C/C | C/T | A/A | T/C | A/T |
| C/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | T/T | C/C | C/C | C/C | A/A | T/T | A/A |
| T/T | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/C | C/C | C/C | T/T | A/A | C/C | T/T |
| T/T | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/C | C/C | C/C | T/T | A/A | C/C | T/T |
| C/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | T/T | C/C | C/C | C/C | A/A | T/T | A/A |
| C/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | T/T | C/C | C/C | C/C | A/A | T/T | A/A |
| T/T | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/C | C/C | C/C | C/T | A/A | T/C | A/T |
| C/C | A/G | T/C | C/T | T/G | T/G | T/T | C/T | C/C | C/C | C/T | A/A | T/C | A/T | |
| C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/T | C/C | A/A | T/T | A/A | |
| T/T | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/C | C/C | C/C | C/T | A/A | T/C | A/T |
| T/T | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/C | C/C | C/C | T/T | A/A | C/C | T/T |
| T/C | C/C | A/G | T/C | C/T | T/G | G/G | T/A | C/T | C/T | C/T | C/C | A/G | A/A | |
| T/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/C | C/T | A/A | T/C | A/T |
| T/T | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/C | C/C | C/C | T/T | A/A | C/C | T/T |
| T/C | C/T | A/G | T/C | C/C | T/G | T/G | T/T | T/T | C/C | C/T | C/C | A/A | T/T | A/A |
| C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/T | C/T | A/A | T/C | A/T | |
| T/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/C | C/T | A/A | T/C | A/T |
| T/C | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/T | C/C | C/T | C/T | A/A | T/C | A/T |
| T/T | C/T | A/G | T/C | C/C | T/G | T/G | T/T | C/T | C/C | C/T | C/T | A/A | T/C | A/T |
| C/C | C/T | A/A | T/T | C/C | T/T | T/T | T/T | T/T | C/C | C/T | C/C | A/A | T/T | A/A |
| T/T | C/C | A/G | T/C | C/T | T/G | T/G | T/A | C/C | C/T | C/C | C/T | A/G | T/C | A/T |
| C/C | A/G | T/C | C/T | T/G | T/G | T/A | C/C | C/T | C/C | C/T | A/G | A/T | ||
| T/T | C/C | A/A | T/T | C/C | T/T | T/T | T/T | C/C | C/C | C/C | T/T | A/A | C/C | T/T |
| T/C | C/C | A/G | T/C | C/T | T/G | T/G | T/A | C/T | C/T | C/T | C/C | A/G | A/A |
> CEUDist
MyHeatmap <- LDheatmap(CEUSNP, CEUDist, LDmeasure = "r",title = "Pairwise LD in r^2", add.map = TRUE, SNP.name = c("rs2283092", "rs6979287"), color = grey.colors(20),name = "myLDgrob", add.key = TRUE)
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