Genefu package

[Ojulari]

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# Minimal reproducible example; please be sure to set verbose=TRUE where possible!

# Output of sessionInfo()

[Ojulari]

I am trying to do a portfolio with the genefu package replicating the tutorial using breastcancervdx but ones I get to a stage in molecular subtype classification this code it gives error error. It doesn’t recognise this (“ surv.obj.PAM50 <- survfit(Surv(data.for.survival.PAM50$months_to_death, data.for.survival.PAM50$vital_status) ~ data.for.survival.PAM50$PAM50)

Secondly for comparing risk prediction once I get to this code it starts giving error as well

here

BIND ALL TOGETHER

res <- rbind(res, rest) } names(ddemo.all) <- dn

Please I need your help as I need to be able to run the complete tutorial with the vdx get me my curve and be able to discuss and create a portfolio for submission Thanks in anticipation of your response

Best regards Halimat

[ChristopherEeles]

Hi @Ojulari,

We are happy to help with your concern.

However, please kindly read the issue template and include all requested information so we get enough context to answer your questions.

Best, Christopher Eeles Software Developer Haibe-Kains Lab

[Ojulari]

Hi ChristopherEeles

For the molecular subtype I have written the code I run and error. data.for.survival.PAM50$months_to_death <- data.for.survival.PAM50$t.os / days.per.month data.for.survival.PAM50$vital_status <- data.for.survival.PAM50$e.os == "1" surv.obj.PAM50 <- survfit(Surv(data.for.survival.PAM50$months_to_death, data.for.survival.PAM50$vital_status) ~ data.for.survival.PAM50$PAM50)

Once I run the above code w.r.t PAM50 and SCMOD2 this is the error given Error in survfit formula(surv(data.for.survival.PAM50$month_to_death,: data has no non-missing observations

and I noticed that the data survival for both has 0 objects of 4 variables for both And I can’t proceed to get the Kaplan Meier curve either.

and I have also written the codes I run and errors generated for risk prediction model.

res <- rbind(res, rest) } names(ddemo.all) <- dn

error message Error in cbind, rest AKURA =sig.score(x=modt, data=ddata, annot = dannot, : Object ‘rest’ not found

looking forward to hear from you soon. Thanks

best regards Halimat

[Ojulari]

Hi ChristopherEles

trust your day is going on well.

please am looking forward to hear from you

thanks in anticipation of your response

[Ojulari]

Hi ChristopherEeles

For the molecular subtype I have written the code I run and error. data.for.survival.PAM50$months_to_death <- data.for.survival.PAM50$t.os / days.per.month data.for.survival.PAM50$vital_status <- data.for.survival.PAM50$e.os == "1" surv.obj.PAM50 <- survfit(Surv(data.for.survival.PAM50$months_to_death, data.for.survival.PAM50$vital_status) ~ data.for.survival.PAM50$PAM50)

Once I run the above code w.r.t PAM50 and SCMOD2 this is the error given Error in survfit formula(surv(data.for.survival.PAM50$month_to_death,: data has no non-missing observations

and I noticed that the data survival for both has 0 objects of 4 variables for both And I can’t proceed to get the Kaplan Meier curve either.

and I have also written the codes I run and errors generated for risk prediction model.

res <- rbind(res, rest) } names(ddemo.all) <- dn

error message Error in cbind, rest AKURA =sig.score(x=modt, data=ddata, annot = dannot, : Object ‘rest’ not found

looking forward to hear from you soon. Thanks

best regards Halimat