search

lvclark / polyRAD

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝
24 stars 8 forks source link

Export_MAPpoly error #39

Closed kaurharpreet-umn closed 1 year ago

kaurharpreet-umn commented 1 year ago

Hello

I am using polyRAD for calling genotypes in alfalfa crop. I have F1 progenies SNP data. I am having issues exporting the data out of polyRAD to run analysis in Mappoly. Here is the error I am getting:

Error in object$posteriorProb[[ploidyIndex, as.character(pld.p)]] : subscript out of bound

Thanks for your help!

Harpreet

lvclark commented 1 year ago

Hi Harpreet,

Would it be possible for you to share with me data and code that I can use to reproduce this error on my own machine? It sounds like a bug in polyRAD but I can't solve it if I can't reproduce it.

Thanks,

Lindsay

kaurharpreet-umn commented 1 year ago

Thank you for your quick response, Lindsay!

Should I use this 'dragonzuela04@gmail.com' to share the files?

lvclark commented 1 year ago

Yes, that works!

kaurharpreet-umn commented 1 year ago

I have shared a link with you to access the files to replicate the error.

lvclark commented 1 year ago

I found the bug in Export_MAPpoly relating to how polyRAD 2.0 tracks ploidy within the object. I will have that fixed and pushed to GitHub momentarily. I also recommend running

mydata3$locTable$Chr <- sub("\\.1$", "", mydata3$locTable$Chr)

to avoid the warning about chromosome names.