gl.report.replicates

[Sandra Erdmann]

Hi All,

I have joined the workshop last month (which was incredibly helpful btw!) and saw the function gl.report.replicates in the script for investigating relatedness. When trying to run this function (dartR version 2.9.7), it said it couldn't find the function. Does it not exist anymore or is there an alternative function available (maybe in dartRverse)??

Thanks,

Sunny

[Bernd.Gruber]

Hi Sunny,

It is in dartR.base (github dev version >0.88)

Cheers, Bernd

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On 6 Apr 2024, at 16:26, Sandra Erdmann <sann...@gmail.com> wrote:



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[Sandra Erdmann]

Thank you Bernd!

I have updated the packages with guidance from here (https://github.com/green-striped-gecko/dartRverse) and after restarting R, I could run the function under version 0.89.

Cheers,

Sunny

[Manuela Cascini]

Hi Luis,

I am using the gl.report.replicates function for the first time and I am rather puzzled by the NA columns results. I copied an extract below, you will see that most samples have around 99% NA.

It seems weirdly high to me, ow would you explain it? 

perc nloc ind1_NA ind2_NA
0.9268293 1230 0.989575 0.9967923
0.9268092 1216 0.9839615 0.9903769
0.9268061 1052 0.8460305 0.9967923
0.9267697 1229 0.9959904 0.989575
0.926749 1215 0.9799519 0.9943865
0.926749 1215 0.9799519 0.9943865
0.9267311 1242 0.9975942 0.9983962

Thanks,

Manuela

[Jose Luis Mijangos]

Hi Manuela,

Yes, the documentation is not clear. The "NA" columns show the call rate not missing data. So, 0.99 means that 1% of loci have missing data. 

Cheers,

Luis

[Manuela Cascini]

Of course, I should have thought about that!

Thanks Luis

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