Dear Researchers,
As per tutorial of adegenet and online r commands, I have used fasta2dnabin and dnabin2genind to import MSA data in fasta format. But how to input population information? I have 115 sequences and want to divide into five populations. I have also failed finding automatic clusters in the step table(pop(x), grp$grp) from adegenet tutorial (http://adegenet.r-forge.r-project.org/files/tutorial-dapc.pdf). I think somehow dnabin2genind cannot handle "-' in the alignment.
There are some good tutorials of adegenet online, but I am unable to follow because of my ignorance of r codes. Kindly help me asap to import my data in r in proper format and perform DAPC analysis with predefined or computed no. of populations.
Regards,
Hi Ashis, Im pretty sure you don't need this answer anymore, but I'll let the tip anyway. Instead to try to convert your sequences in multiple ways I recommend you workaround and simply replace the bases for number or states (A=1, T=2, G=3, C=4, gap = 5, and any other combination as NA). To save time, it would be better if you keep only the polymorphic sites in your file.
Then you can create a txt tab (or wherever) delimited file with ID and POP columns and a collumn for each site as a locus.
You can read it into R as a data frame using read.table() and then use data frame to genind function in adegenet. After that, you can carry on the DAPC analysis.
I hope it helps you or someone else.
Cheers
- Badges
- Science topic
- Similar topics
- Filing