prep_beam_specs function

Prepare beam.specs

Prepare the beam.specs data.frame for BEAM model fitting. Specifies the univariate models needed to compute the BEAMR set p-values.

prep_beam_specs(
  beam.data,
  endpts,
  firth = TRUE,
  adjvars = NULL,
  endptmdl = NULL
)

Arguments

• beam.data: A beam.data object from prep_beam_data
• endpts: A vector of endpoint variable names in main.data
• firth: A logical value. If TRUE (defaul) fit Firth penalized Cox model to account for monotone likelihood in the presence of rare events or predictors. If FALSE fit usual Cox model.
• adjvars: Default NULL, optional vector of adjustment variable names in main.data
• endptmdl: Optional model specification data.frame with endpoint name column called "endpt" and model string column called "mdl"

Returns

The beam.specs object, a data.frame specifying the omics-endpoint association models to be fit

Examples

data(clinf)
data(omicdat)
data(omicann)
data(setdat)
test.beam.data <- prep_beam_data(main.data=clinf, mtx.data=omicdat,
                                 mtx.anns=omicann, set.data=setdat,
                                 set.anns=NULL, n.boot=10, seed=123)
#Without adjustment
prep_beam_specs(beam.data=test.beam.data, endpts=c("MRD29", "OS", "EFS"),
                firth=TRUE)
# With adjustment
prep_beam_specs(beam.data=test.beam.data, endpts=c("OS", "EFS"),
                adjvars=c("MRD29"), firth=TRUE)