SurvivalExperiment {PDATK} | R Documentation

## Constructor for `SurvivalExperiment` Class Builds a `SurvivalExperiment` object, which is just a wrapper for a `SummarizedExperiment` with mandatory survival metadata numeric columns `survival_time` and `event_occurred`.

### Description

Constructor for `SurvivalExperiment` Class

Builds a `SurvivalExperiment` object, which is just a wrapper for a `SummarizedExperiment` with mandatory survival metadata numeric columns `survival_time` and `event_occurred`.

### Usage

    SurvivalExperiment(
      ...,
      survival_time = "survival_time",
      event_occurred = "event_occurred"
    )

### Arguments

`...` | `pairlist` Fall through arguments to the `SummarizedExperiment` constructor. If the first argument to dots is a `SummarizedExperiment`, that object is used instead.
`survival_time` | A `character` vector indicating the column name in `colData` which contains the `integer` number of days a patient has survived since treatment at the time of data collection. If `event_occurred` is 1/TRUE, then this is the number of days the patient lived.
`event_occurred` | A `character` vector indicating the column name in `colData` which contains `logical` or `integer` values where 0/FALSE means a patient is alive and 1/TRUE means a patient is deceased.

### Value

A `SurvivalExperiment` object.

### Examples

    data(sampleICGCmicro)

    # build a SurvivalExperiment from raw data
    ICGCmicro <- SurvivalExperiment(assays=assays(sampleICGCmicro),
      rowData=rowData(sampleICGCmicro), colData=colData(sampleICGCmicro),
      metadata=metadata(sampleICGCmicro), survival_time='survival_time',
      event_occurred='event_occurred')

    # build a SurvivalExperiment from an existig SummarizedExperment
    ICGCmicroSumExp <- as(sampleICGCmicro, 'SummarizedExperiment')
    ICGCmicro <- SurvivalExperiment(ICGCmicroSumExp,
      survival_time='survival_time', event_occurred='event_occurred')

[Package PDATK version 1.2.0 Index]