How to do AMOVA on GBS data
1
0
Entering edit mode
6.0 years ago
jaafari.omid ▴ 80

Hello dears all, Actually I have a vcf file including five populations. This vcf file comes from GBS data and the stacks pipeline. I was going to calculate between and within population diversity based on AMOVA in R (https://rdrr.io/cran/poppr/man/poppr.amova.html) but I got an error which I couldn’t how can I solve that. Here is the command and the error which I have on my face. I will be so grateful if anybody can help me, either with command or any other protocols. Regards, Omid

poppr.amova(omid.genlight, hier = NULL, clonecorrect = FALSE, within = TRUE, dist = omid.D.pop.dist, squared = TRUE, freq = TRUE, correction = "quasieuclid", sep = "-", filter = FALSE, threshold = 0, algorithm = "farthest_neighbor", threads = 1L, missing = "loci", cutoff = 0.05, quiet = FALSE, method = c("ade4", "pegas"), nperm = 0)

Error in poppr.amova(omid.genlight, hier = NULL, clonecorrect = FALSE,: A population hierarchy must be specified

SNP genome R GBS • 2.7k views
ADD COMMENT
0
Entering edit mode

I don't know anything about this R package or the specific function, but it looks like you need to supply an R object to hier. You would need to read the function's documentation. Perhaps the author(s) have a vignette or example data that you should try to see if it works with the example data.

ADD REPLY
0
Entering edit mode

Yes I should define an object but when I read it I couldn't understand what exactly I should to to have this object.

ADD REPLY
0
Entering edit mode

Presumably, you need to specify the hierarchy (structure) of your populations. Granted I haven't read the documentation for the R package or specific function.

ADD REPLY
0
Entering edit mode
2.9 years ago
strive • 0

Hello, may I ask you for advice? I am currently processing GBS data for AMOVA analysis, but errors have been reported and the software cannot run. Could you please leave a contact information for communication?

ADD COMMENT

Login before adding your answer.

Traffic: 2432 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