Why is the “mutation” genomic profile missing from the "Molecular Profile HR Cox analysis" module?

[quiquemedina]

Dear XenaShiny developers,

I noticed that the “mutation” genomic profile is missing from the "Molecular Profile HR Cox analysis" module.

Since the mutation profile is available in the log_rank survival analysis, I am unsure why the profile is missing from the selection options in the HR Cox analysis. • HR Cox analysis: The "mutation" profile option is absent. • log_rank survival analysis: The "mutation" profile option is present.

Specificaly: UCSCXenaShiny v1.1.8 based on UCSCXenaTools v1.4.8

In R manual,that data type also missing: data_type: choose gene profile type, including "mRNA","transcript","methylation","miRNA","protein","cnv"

R Cox analysis: mutation ´profile option is absent

Log rank analysis: mutation ´profile option is present

[lishensuo]

Thanks for the suggestion. We have added the 'mutation' profile for the Cox analysis of TCGA module in the latest update.

[quiquemedina]

Great! I checked it, and it's working fine. Please keep in mind to update the info in the "help" (R studio), so the clients can call it.

data_type | choose gene profile type, including "mRNA","transcript","methylation","miRNA","protein","cnv" to include "mutation"

vis_unicox_tree( Gene = "TP53", measure = "OS", data_type = "mutation", use_optimal_cutoff = FALSE, values = c("grey", "#E31A1C", "#377DB8"), opt_pancan = .opt_pancan )

Regards, Enrique

[lishensuo]

Thanks for your reminder. We will optimize it in the next commit.