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Last data update: 2014.03.03

R: Extract Survival Information From RTCGA.clinical Datasets

survivalTCGA

R Documentation

Extract Survival Information From RTCGA.clinical Datasets

Description

Extracts survival information from clicnial datasets from TCGA project.

Usage

survivalTCGA(..., extract.cols = NULL, extract.names = FALSE,
  barcode.name = "patient.bcr_patient_barcode",
  event.name = "patient.vital_status",
  days.to.followup.name = "patient.days_to_last_followup",
  days.to.death.name = "patient.days_to_death")

Arguments

`...`	A data.frame or data.frames from TCGA study containing clinical informations. See clinical.
`extract.cols`	A character specifing the names of extra columns to be extracted with survival information.
`extract.names`	Logical, whether to extract names of passed data.frames in `...`.
`barcode.name`	A character with the name of `bcr_patient_barcode` which differs between TCGA releases. By default is the name from the newest release date `tail(checkTCGA('Dates'),1)`.
`event.name`	A character with the name of `patient.vital_status` which differs between TCGA releases. By default is the name from the newest release date `tail(checkTCGA('Dates'),1)`.
`days.to.followup.name`	A character with the name of `patient.days_to_last_followup` which differs between TCGA releases. By default is the name from the newest release date `tail(checkTCGA('Dates'),1)`.
`days.to.death.name`	A character with the name of `patient.days_to_death` which differs between TCGA releases. By default is the name from the newest release date `tail(checkTCGA('Dates'),1)`.

Value

A data.frame containing information about times and censoring for specific bcr_patient_barcode. The name passed in barcode.name is changed to bcr_patient_barcode.

Issues

If you have any problems, issues or think that something is missing or is not clear please post an issue on https://github.com/RTCGA/RTCGA/issues.

Note

Input data.frames should contain columns patient.bcr_patient_barcode, patient.vital_status, patient.days_to_last_followup, patient.days_to_death or theyir previous equivalents. It is recommended to use datasets from clinical.

Author(s)

Marcin Kosinski, m.p.kosinski@gmail.com

Examples


## Extracting Survival Data
library(RTCGA.clinical)
survivalTCGA(BRCA.clinical, OV.clinical, extract.cols = "admin.disease_code") -> BRCAOV.survInfo

# first munge data, then extract survival info
library(dplyr)
BRCA.clinical %>%
    filter(patient.drugs.drug.therapy_types.therapy_type %in%
               c("chemotherapy", "hormone therapy")) %>%
    rename(therapy = patient.drugs.drug.therapy_types.therapy_type) %>%
    survivalTCGA(extract.cols = c("therapy"))  -> BRCA.survInfo.chemo
                 
# first extract survival info, then munge data                  
    survivalTCGA(BRCA.clinical, 
                 extract.cols = c("patient.drugs.drug.therapy_types.therapy_type"))  %>%
    filter(patient.drugs.drug.therapy_types.therapy_type %in%
               c("chemotherapy", "hormone therapy")) %>%
    rename(therapy = patient.drugs.drug.therapy_types.therapy_type) -> BRCA.survInfo.chemo

## Kaplan-Meier Survival Curves
kmTCGA(BRCAOV.survInfo, explanatory.names = "admin.disease_code",  pval = TRUE)

kmTCGA(BRCAOV.survInfo, explanatory.names = "admin.disease_code", main = "",
       xlim = c(0,4000))
 
kmTCGA(BRCA.survInfo.chemo, explanatory.names = "therapy", xlim = c(0, 3000), conf.int = FALSE)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RTCGA)
Welcome to the RTCGA (version: 1.2.2).
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RTCGA/survivalTCGA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: survivalTCGA
> ### Title: Extract Survival Information From RTCGA.clinical Datasets
> ### Aliases: survivalTCGA
> 
> ### ** Examples
> 
> 
> ## Extracting Survival Data
> library(RTCGA.clinical)
> survivalTCGA(BRCA.clinical, OV.clinical, extract.cols = "admin.disease_code") -> BRCAOV.survInfo
> 
> # first munge data, then extract survival info
> library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> BRCA.clinical %>%
+     filter(patient.drugs.drug.therapy_types.therapy_type %in%
+                c("chemotherapy", "hormone therapy")) %>%
+     rename(therapy = patient.drugs.drug.therapy_types.therapy_type) %>%
+     survivalTCGA(extract.cols = c("therapy"))  -> BRCA.survInfo.chemo
>                  
> # first extract survival info, then munge data                  
>     survivalTCGA(BRCA.clinical, 
+                  extract.cols = c("patient.drugs.drug.therapy_types.therapy_type"))  %>%
+     filter(patient.drugs.drug.therapy_types.therapy_type %in%
+                c("chemotherapy", "hormone therapy")) %>%
+     rename(therapy = patient.drugs.drug.therapy_types.therapy_type) -> BRCA.survInfo.chemo
> 
> ## Kaplan-Meier Survival Curves
> kmTCGA(BRCAOV.survInfo, explanatory.names = "admin.disease_code",  pval = TRUE)
> 
> kmTCGA(BRCAOV.survInfo, explanatory.names = "admin.disease_code", main = "",
+        xlim = c(0,4000))
>  
> kmTCGA(BRCA.survInfo.chemo, explanatory.names = "therapy", xlim = c(0, 3000), conf.int = FALSE)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>