Question: Help making ADMIXTURE output digestible
1
gravatar for devenvyas
5.0 years ago by
devenvyas640
Stony Brook
devenvyas640 wrote:

I am new to the program ADMIXTURE.

I am running it from K=1 to K=20 on a set of 2033 individuals and 276,899 SNPs post-LD-pruning. The sample order is based on the default order in the dataset I downloaded, so population members are not necessarily back-to-back and related populations are not necessarily listed near each other.

Ideally, in the morning I will have a set of 40 *.Q files (20 with CV and bootstrap and 20 without), so in preparation I am trying to figure out how to graph them with the bars in a meaningful order. I was wondering if anyone had suggestions on how to this (or general suggestions about managing ADMIXTURE output).

Thanks!

 

 

 

admixture • 3.2k views
ADD COMMENTlink modified 3.6 years ago by beausoleilmo320 • written 5.0 years ago by devenvyas640

I have the exact same question! Here is a similar one: Can't figure out order of output rows in ADMIXTURE

ADD REPLYlink written 3.6 years ago by beausoleilmo320
0
gravatar for beausoleilmo
3.6 years ago by
beausoleilmo320
McGill University
beausoleilmo320 wrote:

I found this website explaining how to do the full analysis. Basically, you have to look in the .fam file. You can import this file in R like this: fam = read.table("~/path-to-the-file/my_analysis.fam"). After that I was reusing the first column and rename the rows of your .Q file: tbl = read.table("~/path-to-the-file/my_analysis.Q"). Use this dataset to print your barplot!

ADD COMMENTlink written 3.6 years ago by beausoleilmo320
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1351 users visited in the last hour