plotting allele frequencies generated using vcftools
1
1
Entering edit mode
5.2 years ago
Dtriumph ▴ 30

Hi,

I'm trying to plot allele frequency of my GBS data. I could generate the allele frequencies for each chromosome separately using vcftools and output files are in .frq format. I couldn't find a specific R package that help plot the data.

I appreciate any help with links to relevant R packages...

Thanks!

GWAS genome plots SNP vcftools • 4.1k views
ADD COMMENT
0
Entering edit mode

Need the exact same thing. Did you ever solve this?

ADD REPLY
4
Entering edit mode
5.2 years ago
venu 7.0k

If you would like to get an overview of the AF distribution, you can use simple density function from R. Something like following

# read data into R object (ex: dat)

plot(density(dat$AF)) #AF - field which contains AF values
ADD COMMENT
0
Entering edit mode

Thanks for your answer....

ADD REPLY

Login before adding your answer.

Traffic: 1729 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