Pairwise linkage disequilibrium
1
0
Entering edit mode
5.4 years ago
ivenisec • 0

I have a file with hundreds of rsIDs in pairs. I want to test if each pair is in linkage disequilibrium. Is there a tool that can calculate all of them at the same time? My file looks like this: (the reference sequence is hg19)

rs4648356    rs6687680

rs227163      rs12407642

rs227163      rs10489448

rs616488      rs1755594

Thanks for the help!

linkage disequilibrium rsID pairwise • 2.3k views
ADD COMMENT
0
Entering edit mode

in LD in what population? Do you also have a file with genotypes?

ADD REPLY
1
Entering edit mode
5.4 years ago
reza.jabal ▴ 500

This is a shut in the dark unless you'd like to check pairwise LD in one of the HapMap reference populations. The rest is relatively straightforward in Bioconductor:

> library(LDheatmap)
> data("CEUData")
> MyHeatmap <- LDheatmap(CEUSNP, CEUDist, LDmeasure = "r",
+ title = "Pairwise LD in r^2", add.map = TRUE,
+ SNP.name = c("rs4648356", "rs6687680"), color = grey.colors(20),
+ name = "myLDgrob", add.key = TRUE)

You can write a bash script to read from your snpList.file and pass it to the R. You may find this helpful!

ADD COMMENT

Login before adding your answer.

Traffic: 2585 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6