Extract Survival Information from Datasets Included in RTCGA.clinical and RTCGA.clinical.20160128 Packages

Extracts survival information from clicnial datasets from TCGA project.

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.

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.

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.

See also

RTCGA website http://rtcga.github.io/RTCGA/articles/Visualizations.html.

Other RTCGA: RTCGA-package, boxplotTCGA, checkTCGA, convertTCGA, createTCGA, datasetsTCGA, downloadTCGA, expressionsTCGA, heatmapTCGA, infoTCGA, installTCGA, kmTCGA, mutationsTCGA, pcaTCGA, readTCGA, theme_RTCGA

Examples

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

## 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))

# 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


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