request support

[Kndalem Yaregal]

Hi,

In have have genotyped one sample two to three times and I want to know within sample difference by what means I run this?

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Thank you!

Kind regards,

Kndalem Yaregal 

MSc. Student in Plant Breeding and Genetics |Wollo University 

Plant Breeder |Sekota Dryland Agricultural Research Center  in Amhara Agricultural Research Institute 

Email (Alt): 21ethi...@gmail.com 

skype: Kndalem. Yaregal

 Mobile: +251916899864, Ethiopia

"Improving the Dryland for Mind Glad."

 "Make a positive impact in our community!"

[Bernd.Gruber]

Hi,

 

A quick way to do it is creating a table between pairs of genotypes.

 

i <- which(indNames(gl)==”ind1”)

j <- which(indNames(gl)=”ind2”)

 

tt <- table(as.matrix(gl[i,]), as.matrix(gl[j,], useNA=”always”)

tt

 

sum(diag(tt))/sum(tt)

 

This creates a confusion table between the individual i and j. on the diagonal you find the numbers genotypes 0,1,2 are matching, off the diagonal the not matching genotypes.

 

We should create a function that does all pairs provided. (as I use it quite a lot). I have also a function that calculates the error rate for repeated genotypes if you are interested.

 

Cheers, Bernd

 

Ps. If you copy the code above make sure you replace the quotes but straight ones.

 

 

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Sent: Thursday, 18 September 2025 3:41 PM
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Subject: [dartR] request support

 

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[Kndalem Yaregal]

thank you so much for your assistance 

Yes, I am interesting onwhat you say (repeating. could you send me?

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