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DarioS / ClassifyR

A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing
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No vignette/examples for survival analysis #87

Closed adam2o1o closed 1 year ago

adam2o1o commented 1 year ago

Hi there, I'd like to use ClassifyR for survival analysis but there arent any examples I can find. If you could help that would be great, thanks

DarioS commented 1 year ago

The package is near the time limit for Bioconductor checking but I think I can squeeze in some. Perhaps using MetaGxBreast. But it's basically just specifying the outcome in a couple of different ways, as mentioned in Quick Start section.

crossValidate must also be supplied with outcome, which represents the prediction to be made in a variety of ways.

  • A factor that contains the class label for each observation. classes must be of length n.
  • A character of length 1 that matches a column name in a data frame which holds the classes. The classes will automatically be removed before training is done.
  • A Surv object of the same length as the number of samples in the data which contains information about the time and censoring of the samples.
  • A character vector of length 2 or 3 that each match a column name in a data frame which holds information about the time and censoring of the samples. The time-to-event columns will automatically be removed before training is done.
nick-robo commented 1 year ago

Maybe you could set eval=FALSE for some heavier operations or examples. Only BiocCheck complains about this and it is not run on the package after release.

DarioS commented 1 year ago

Article showing survival analysis of METABRIC breast cancer clinical data added. Please close if sufficient or suggest changes.