Create contingency table for a specific set of adverse events

Build contingency tables for disproportionality analysis focusing on a specific set of adverse events (e.g., irAEs). This function extends faers_phv_table to handle composite event definitions.

faers_phv_composite(.object, .event_set, ..., .full, .object2)

# S4 method for class 'FAERSascii,ANY,FAERSascii,missing'
faers_phv_composite(
  .object,
  .event_set,
  .event_type = "pt",
  ...,
  .full,
  .object2
)

# S4 method for class 'FAERSascii,ANY,missing,FAERSascii'
faers_phv_composite(
  .object,
  .event_set,
  .event_type = "pt",
  ...,
  .full,
  .object2
)

faers_phv_signal_composite(.object, ...)

# S4 method for class 'FAERSascii'
faers_phv_signal_composite(
  .object,
  .event_set,
  .methods = NULL,
  ...,
  .phv_signal_params = list(),
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

.object

A FAERSascii object. The unique number of primaryids from .object will be regarded as n1..

.event_set

A character vector of PT terms or a logical expression that defines the set of adverse events of interest.

...

Other arguments passed to specific methods.

.full

A FAERSascii object with data from full database.

.object2

A FAERSascii object with data from another interested drug.

.event_type

A character string specifying the type of adverse event to use. Must be one of the two specific literal values: "pt" (Preferred Term) or "soc_name" (System Organ Class name). Any other value will cause an error. Defaults to "pt".

.methods

Analysis methods to use (passed to phv_signal).

.phv_signal_params

Other arguments passed to phv_signal.

BPPARAM

An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation.

Value

A data.table object with contingency tables for the specified event set.

See also

phv_signal