gbm, assayNames errors in dataman2017.Rmd

[gillsignals]

Two errors are present that break the code in the "Working with TCGA mutation data" section.

When defining the gbm object in dataman2017.Rmd, there are errors. The gbm object is still defined, but I am not sure it is successfully updated.

>gbm = updateObject(gbm)
>gbm
A MultiAssayExperiment object of 12 listed
 experiments with user-defined names and respective classes. 
 Containing an Error in vapply(object, FUN = function(obj) { : values must be length 1,
 but FUN(X[[3]]) result is length 0
Error during wrapup: cannot get a slot ("slots") from an object of type "NULL"

This may be related to a downstream error in assayNames. :

> mut = experiments(gbm)[["Mutations"]]
> head(assayNames(mut))
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'assayNames' for signature '"RangedRaggedAssay"'

Later components of the TCGA code rely on mut and cannot be performed due to current errors.

[vjcitn]

Can you send me the sessionInfo() of the session you are working with? I think there is also a problem with ldblock::stack1kg that will necessitate update to that package.

…

On Thu, Aug 15, 2019 at 7:09 PM gillsignals ***@***.***> wrote: Two errors are present that break the code in the "Working with TCGA mutation data" section. When defining the gbm object in dataman2017.Rmd, there are errors. The gbm object is still defined, but I am not sure it is successfully updated. >gbm = updateObject(gbm) >gbm A MultiAssayExperiment object of 12 listed experiments with user-defined names and respective classes. Containing an Error in vapply(object, FUN = function(obj) { : values must be length 1, but FUN(X[[3]]) result is length 0 Error during wrapup: cannot get a slot ("slots") from an object of type "NULL" This may be related to a downstream error in assayNames. : > mut = experiments(gbm)[["Mutations"]] > head(assayNames(mut)) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'assayNames' for signature '"RangedRaggedAssay"' Later components of the TCGA code rely on mut and cannot be performed due to current errors. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#75?email_source=notifications&email_token=ABDI5QQASTFJU6MRD5OR3RTQEXOZHA5CNFSM4IMCS5LKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HFRGNCA>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABDI5QUNMZXUNKALNWOMPITQEXOZHANCNFSM4IMCS5LA> .

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[gillsignals]

Apologies for the omission - it was the same sessionInfo from issue 73 where I reported the issue to ldblock::stack1kg.

[vjcitn]

These observations are correct. The solution is to introduce curatedTCGAData package and rewrite the GBM-oriented elements. I will do this in the next few days.

[vjcitn]

I have introduced dataman2019.Rmd in github and in the book pages. It tests successfully
on several systems. If you are able to verify please close this issue @gillsignals

Thanks!

[gillsignals]

This fixes the issue with gbm. Thanks!