TESS format from genlight

[Susan Miller]

Hi,

Does anyone know how to convert a genlight object to a format suitable for tess3r?

the required format is: 1 row per individual, snps coded as 0, 1 and 2

I've tried quite a few of the options in dartR and I can't find one that gives this format. Any suggestions?

thanks,

Susan

[Jose Luis Mijangos]

Hi Susan,

Can you try the code below:

Cheers,

Luis 

devtools::install_github("bcm-uga/TESS3_encho_sen")
library(tess3r)
t1 <- gl.filter.callrate(platypus.gl,threshold = 1)
genotype <- as.matrix(t1)
coordinates <- as.matrix(t1$other$latlon)
tess3.obj <- tess3(X = genotype, coord = coordinates, K = 1:3,
                   method = "projected.ls", ploidy = 2, openMP.core.num = 1) 

[Bernd.Gruber]

Would not be a simple

 

as.matrix(gl)

 

do the trick?

 

Cheers, Bernd

 

 

P.S. In case you need them as strings per row that might help

 

> glm <-(as.matrix(possums.gl[1:5,1:7]))

>

> glms <- apply(glm, 1, function(x) paste(x, collapse = ""), simplify = F)

>

> rglms <- do.call(rbind, glms)

> rglms

  [,1]    

1 "1212221"

2 "1111110"

3 "2020111"

4 "0120010"

5 "1212221"

> 

 

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