add_coldata_survival.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/add_coldata_survival.R
\name{add_coldata_survival}
\alias{add_coldata_survival}
\title{Add columns for Survival Analysis}
\usage{
add_coldata_survival(
  summarized_experiment,
  time_to_event = "days_to_death",
  time_follow_censor = "days_to_last_follow_up",
  event = "vital_status",
  event_names = c("alive", "dead"),
  drop_na = T,
  na_if = "not reporetd"
)
}
\arguments{
\item{summarized_experiment}{A SummarizedExperiment object or a data frame}

\item{time_to_event}{Character - column name of time to the event}

\item{time_follow_censor}{Character - column name of time of last follow up or right censoring}

\item{event}{Character - column name of event (vital_status)}

\item{event_names}{Character - chracter vector with two instances representing the levels of "event". Default = c("alive", "dead")}

\item{drop_na}{Logical - drop rows with missing values in event or time of event?}

\item{na_if}{Character - mark character "na_if" as NA}
}
\description{
This function calculates event times from a data frame. Data from TCGA is not in the right format for survival analysis.
}
\details{
Column event needs to consist of 2 factor levels: "alive" and "dead".
}