vafCompare issue

[NewBee100]

Hi PoissonAlien, I constantly get an error message when using vafCompare on my own set of mutational samples.
I've tried it on the TCGA studies as below, get the same error.

Command

> TCGAmutations::tcga_load(study = "LUAD") -> LUAD
 > TCGAmutations::tcga_load(study = "LUSC") -> LUSC
 > vafCompare(m1 = LUAD, m2 = LUSC)

t_vaf field is missing, but found t_ref_count & t_alt_count columns. Estimating vaf..
t_vaf field is missing, but found t_ref_count & t_alt_count columns. Estimating vaf..
Error in if (!is.na(sig)) { : the condition has length > 1

Is there a way to fix this?

Many thanks!

[NewBee100]

Hi,

Any chance of an answer? It is a great package, it's a shame that some great features like vafcompare do not work, at least in my case.

[PoisonAlien]

Hello! Sorry for my tardy response. Things have gotten really busy recently - I have not been able to answer any of the issues. It will be back to normal soon from next week.

[NewBee100]

Ok, that would really great, thanks you!!!

[FriederikeHanssen]

HI! I am running into the same thing. Anyone figured out what the cause could be? :)

[ShixiangWang]

HI! I am running into the same thing. Anyone figured out what the cause could be? :)

This is typically caused by the R4.2 version, as it would no longer support a vector as input of if expression.

[FriederikeHanssen]

Thank you :) I will try to downgrade the R version

[ShixiangWang]

Thank you :) I will try to downgrade the R version

I will put a quick PR on this, please wait.

[NewBee100]

It would be great for this to be resolved soon, thank you!!

[ShixiangWang]

@NewBee100 @FriederikeHanssen Please try installing the PR and restart R to check if it works.

remotes::install_github("PoisonAlien/maftools#880")

[NewBee100]

I can only try late in the afternoon today . Will let you know. FriederikeHanssen, are you able to try earlier than that? Thanks

[FriederikeHanssen]

works 🚀 thanks a lot :)

[FriederikeHanssen]

Just FYI: using this installation mafbarplot is not working anymore. (could not find function "mafbarplot") which worked fine with the latest install from bioconda.

[ShixiangWang]

@FriederikeHanssen Thanks for pointing this out. I created a PR on wrong branch, I will update and let you known.

[ShixiangWang]

Please use the new PR, sorry for that.

remotes::install_github("PoisonAlien/maftools#881")

[NewBee100]

Hi, It does not work for me, now the error message is ``Error in graphics::layout(p, ...) : argument "p" is missing, with no default `

I don't know what this means or how to solve this..

[ShixiangWang]

@NewBee100 Could you put all your commands and output for reproducing the error?

[NewBee100]

Good evening , I've tried again, now it worked 🤔 I had, possibly, too many other packages loaded, a conflict issue? ? Anyway, it's good now. Thank you!!!