survivalTCGA | R Documentation |
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" )
... |
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 |
event.name |
A character with the name of |
days.to.followup.name |
A character with the name of |
days.to.death.name |
A character with the name of |
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
.
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.
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.
Marcin Kosinski, m.p.kosinski@gmail.com
Marcin Kosinski, m.p.kosinski@gmail.com
RTCGA website http://rtcga.github.io/RTCGA/articles/Visualizations.html.
Other RTCGA:
RTCGA-package
,
boxplotTCGA()
,
checkTCGA()
,
convertTCGA()
,
datasetsTCGA
,
downloadTCGA()
,
expressionsTCGA()
,
heatmapTCGA()
,
infoTCGA()
,
installTCGA()
,
kmTCGA()
,
mutationsTCGA()
,
pcaTCGA()
,
readTCGA()
,
theme_RTCGA()
## 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)
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