clinical enrichment

[batis2ta]

Salute, any idea why I get subscipt out of bounds error?

> fab.ce <- clinicalEnrichment(maf = laml, clinicalFeature = 'Histology', useCNV = FALSE, minMut = 1)
Sample size per factor in Histology:

               ADC Adenosaquam”ses_Ca      basaloides_Ca                SCC 
                13                  1                  1                  5 
Error in `[.default`(cd.tbl, c("WT", "Mutant"), c(y, "Other")) : 
  subscript out of bounds

[PoisonAlien]

Is it possible share your files ? Its hard for me to guess the issue. You can mail (anandmt3@gmail.com) me if you dont want to share here.

[batis2ta]

I am affraid I am not allowed to send or share the data.

I tried to go through the function and sent you the log, maybe it would help you, but I understand might still be hard to guess. Best

[clersdom]

Hi, I am having the same error. Did you manage to solve this? Thanks.

[PoisonAlien]

Hi @clersdom , Could you share a reproducible example so that I can figure out the issue? My discussion with @batis2ta could not be resolved due to lack of an example data set. Thanks again @batis2ta - and sorry I couldn't help you with this.

[clersdom]

Hi @PoisonAlien , I can send you an email.

[PoisonAlien]

Yes, that would be great. You can send it to anandmt3@gmail.com If it contains sensitive information, you can change barcodes and other related fields. I only need those required fields mentioned in the vignette.

[batis2ta]

Thanks to both of you. I could not send my data to Anand because it is against our policies. I would appreciate if you could share the solution with us.

best regards

On Fri, Jan 25, 2019 at 10:52 AM Anand Mayakonda notifications@github.com wrote:

Yes, that would be great. You can send it to anandmt3@gmail.com

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/PoisonAlien/maftools/issues/225#issuecomment-457517623, or mute the thread https://github.com/notifications/unsubscribe-auth/AlRnEt148dS4ZoWqOTVASvAzwm-8moKtks5vGtPagaJpZM4Z3hFI .

-- Dr. med. Sayedmohammad Hasheminasab, Translational Radiation Oncology

German Cancer Research Center (DKFZ)

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 56 6075

[batis2ta]

Any updates?

[PoisonAlien]

Hi @batis2ta , Sorry, I still have trouble reproducing the error :|

[batis2ta]

Hi I went a little bit further, the error comes from g = unique(genesToBarcodes(maf = maf, genes = z, justNames = TRUE)[[1]]) or actually genesToBarcodes(maf = maf, genes = z, justNames = TRUE) where it says

Error in as.character.default(genes) : no method for coercing this S4 class to a vector

at this point x is the maf object and the whole this could not be coerce to a character does this make sence?

[PoisonAlien]

Okay, I can replicate the issue with a synthetic data similar to yours. I will fix it soon. Its an issue with contingency table.

[PoisonAlien]

Hi, I have fixed it. Could you please try and let me know. You will have to install from GitHub.

[batis2ta]

thanks a lot now I see that the erros is Sample size per factor in Overall_Survival_Status:

0 1 7 7 Error in bmerge(i, x, leftcols, rightcols, io, xo, roll, rollends, nomatch, : x.'cf' is a character column being joined to i.'Feature_1' which is type 'integer'. Character columns must join to factor or character columns.

[PoisonAlien]

Okay I think this is primarily due to values in Overall_Survival_Status being integer/numeric. If its not of trouble, can you change them to characters like Dead and Alive and see if that fixes the issue ? This function wasnt intended to work on numeric data as its sole purpose was to perform enrichment on categorical data.

[batis2ta]

Yes sure I did that and it worked. I might have been a little low on coffein.

[PoisonAlien]

No problem. We have all been there :)