Question: plotting allele frequencies generated using vcftools
1
gravatar for Dtriumph
2.6 years ago by
Dtriumph30
Dtriumph30 wrote:

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!

vcftools snp plots gwas genome • 1.9k views
ADD COMMENTlink modified 2.6 years ago by venu6.2k • written 2.6 years ago by Dtriumph30

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

ADD REPLYlink written 2.6 years ago by porkbellydotcom0
3
gravatar for venu
2.6 years ago by
venu6.2k
Germany
venu6.2k wrote:

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 COMMENTlink written 2.6 years ago by venu6.2k

Thanks for your answer....

ADD REPLYlink written 2.6 years ago by Dtriumph30
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