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EuracBiomedicalResearch / FamAgg

This is the development version of the FamAgg Bioconductor package.
https://EuracBiomedicalResearch.github.io/FamAgg
MIT License
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Error in plotPed() function #30

Open KimBruijns opened 2 years ago

KimBruijns commented 2 years ago

Hi!

When running this code: mbsub <- pedigfinal[pedigfinal$famid %in% 7:10, ] mbsub<-rename(mbsub, "family"="famid", "id"="Indiv", "father"="Sire", "mother"="Dam", "sex"="Sex") mbped <- mbsub[, c("family", "id", "father", "mother", "sex")] fad <- FAData(pedigree = mbped) plotPed(fad, family = "9")

The function plotPed() from package::FamAgg is not working (the rest works and creates an FAData object) and returns this error: "Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘plotPed’ for signature ‘"character" ".

I thought it might be because of masked objects but specifying the package to use does not help.

Thank you for your help!

jorainer commented 2 years ago

Dear Kim,

really sorry for the very late reply. Was on holidays and am now on a conference. I'll have a look into this soon.

jorainer commented 2 years ago

Can you please verify that fad is indeed a FAData? I.e. report here the output of class(fad)? And maybe also of class(mbped)?

Finally, maybe it's because family 9 consists only of a single member and subsetting drops from a two-dimensional data structure to a character. Can you maybe also provide this information:

sum(mbped[, "family"] == "9")

My guess would be that during subsetting to family 9 somehow the dimensions (or the FAData object) gets lost. I also assume that plotPed works for other families?