data conversion to format for the package introgress

[Gabriella Scatà]

Hi,

I know this is probably too much of a request, but any chance that there is a function in dartR or a way to convert the genlight object to a data format compatible with this function (package introgress):

est.h = finds maximum likelihood estimates of hybrid index as described by Buerkle (2005)

https://rdrr.io/cran/introgress/man/est.h.html --> 

introgress.data may either be the list that is returned by the function prepare.data, or, if fixed=TRUE, introgress.data may simply be a matrix or array providing counts of the number of alleles derived from parental population 1 for each admixed individual.

https://rdrr.io/cran/introgress/man/prepare.data.html -->

Genotypic data for individuals are provided in admix.gen, a data object with genotypes for each individual at each locus in the format ‘A/D’ or ‘110/114’ for co-dominant data, ‘A’ or ‘hap1b’ for haploid data, and ‘0’ or ‘1’ for dominant data. In other words, for co-dominant and haploid data alleles can be encoded by any simple character string. Each row should contain data for a locus and columns should correspond to individuals. Missing data should be entered as ‘NA/NA’ or ‘NA’ for co-dominant and haploid / dominant data, respectively.

I am assuming SNPs are generally assumed to be codominant, correct?

Thank you as usual!

Best,

Gabriella

[Jose Luis Mijangos]

Hi Gabriella,

We don't have a function to convert to this package. The package is not longer maintained, so I think it is not wroth it to create a conversion function.

If you are interested in identifying hybrids, you can try the dartR function "gl.nhybrids".

Cheers,

Luis

[Gabriella Scatà]

Thank you.

I was looking actually at ways to define the hybrids detected...whether they are F1/2/3.

That's why I was looking at that package. But I will try new hybrids first.

Thanks

Best,

Gabriella