SurvivalExperiment: Constructor for 'SurvivalExperiment' Class Builds a...
In bhklab/PDATK: Pancreatic Ductal Adenocarcinoma Tool-Kit

Description Usage Arguments Value Examples

View source: R/class-SurvivalExperiment.R

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.

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

`...`	`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.

A SurvivalExperiment object.

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')