Question: the function of readVCF in PopGenome R package
0
gravatar for mike229lin
5 months ago by
mike229lin10
mike229lin10 wrote:

Hello

I'm using PopGenome R package to calculate Fst with vcf files. I met some problems during the protocol

First, I want to analyze whole genome level data. In the manual of PopGenome, it says I should input a specific chromosome or scaffold name. If I want to generate Fst of whole genome, what should I input? The function of read data seems unavailable for me after I tried many times using the function .

Second, how can I set the "numcol" column if I have 1.7*10E7 SNP sites in my data?

I have about 7000 scaffolds in my reference genome, it seems I should write a R script to make PopGenome package calculate Fst ?

fst popgenome R vcf • 272 views
ADD COMMENTlink modified 4 months ago by Biostar ♦♦ 20 • written 5 months ago by mike229lin10
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: 817 users visited in the last hour