BEAMR (version 1.1.0)

prep_beam_specs: Prepare beam.specs

Description

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

Usage

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

Value

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

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"

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)