Combing population information from other file in Poppr

[RN Sarma]

I have a VCF file of 100000 SNP markers and 196 genotypes.  I have determined the population structure in other programme and saved the genotype-wise population information in a txt file.  If I want to go for AMOVA in poppr how to proceed with using the two files?

Please suggest.

[Zhian Kamvar]

Import the population structure in R as a data frame and then use the `strata()` function to add the data frame (see https://rdrr.io/cran/adegenet/man/strata-methods.html for details).

For example, if you have VCF file called "population.vcf" and your populations structure file is called "population-data.txt" and it's comma-delimited, you can use:

vcf <- vcfR::read.vcfR("population.vcf")

gid <- vcfR::vcfR2genlight(vcf)

# if you want a genind object (8X larger memory footprint), you can use vcfR::vcfR2genind(vcf, return.alleles = TRUE)

population_strata <- read.csv("population-data.txt", header = TRUE)
strata(gid) <- population_strata # this will set the strata based on the column names of your stratifications

On Thu, Jun 29, 2023 at 12:11 AM 'RN Sarma' via poppr <po...@googlegroups.com> wrote:

I have a VCF file of 100000 SNP markers and 196 genotypes.  I have determined the population structure in other programme and saved the genotype-wise population information in a txt file.  If I want to go for AMOVA in poppr how to proceed with using the two files?

Please suggest.

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[Zhian Kamvar]

This would be a table of population information for each individual in rows across strata in columns. 

On Thu, Jul 20, 2023 at 19:08 RN Sarma <ramendr...@aau.ac.in> wrote:

What will information should I have in "population-data.txt" as you have suggested?

Ramen

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Warm regards,

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Dr R N Sarma
Professor
Department of Plant Breeding and Genetics
Assam Agricultural University
Jorhat-785013
Assam, India

Orcid id: 0000-0002-9106-7926
web: www.aau.ac.in; Phone: +91- 9435350529(M)
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[RN Sarma]

I will try it. Thank you