TCGAanalyze_survival: Creates survival analysis

In BioinformaticsFMRP/TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Creates survival analysis

Description

Creates a survival plot from TCGA patient clinical data using survival library. It uses the fields days_to_death and vital, plus a columns for groups.

Usage

TCGAanalyze_survival(
  data,
  clusterCol = NULL,
  legend = "Legend",
  labels = NULL,
  risk.table = TRUE,
  xlim = NULL,
  main = "Kaplan-Meier Overall Survival Curves",
  ylab = "Probability of survival",
  xlab = "Time since diagnosis (days)",
  filename = "survival.pdf",
  color = NULL,
  height = 8,
  width = 12,
  dpi = 300,
  pvalue = TRUE,
  conf.int = TRUE,
  ...
)

Arguments

data	TCGA Clinical patient with the information days_to_death
clusterCol	Column with groups to plot. This is a mandatory field, the caption will be based in this column
legend	Legend title of the figure
labels	labels of the plot
risk.table	show or not the risk table
xlim	x axis limits e.g. xlim = c(0, 1000). Present narrower X axis, but not affect survival estimates.
main	main title of the plot
ylab	y axis text of the plot
xlab	x axis text of the plot
filename	The name of the pdf file.
color	Define the colors/Pallete for lines.
height	Image height
width	Image width
dpi	Figure quality
pvalue	show p-value of log-rank test
conf.int	show confidence intervals for point estimates of survival curves.
...	Further arguments passed to ggsurvplot.

Value

Survival plot

Examples

 # clin <- GDCquery_clinic("TCGA-BRCA","clinical")
 clin <- data.frame(
      vital_status = c("alive","alive","alive","dead","alive",
                       "alive","dead","alive","dead","alive"),
      days_to_death = c(NA,NA,NA,172,NA,NA,3472,NA,786,NA),
      days_to_last_follow_up = c(3011,965,718,NA,1914,423,NA,5,656,1417),
      gender = c(rep("male",5),rep("female",5))
 )
TCGAanalyze_survival(clin, clusterCol="gender")
TCGAanalyze_survival(clin, clusterCol="gender", xlim = 1000)
TCGAanalyze_survival(clin,
                     clusterCol="gender",
                     risk.table = FALSE,
                     conf.int = FALSE,
                     color = c("pink","blue"))
TCGAanalyze_survival(clin,
                     clusterCol="gender",
                     risk.table = FALSE,
                     xlim = c(100,1000),
                     conf.int = FALSE,
                     color = c("Dark2"))

BioinformaticsFMRP/TCGAbiolinks documentation built on April 12, 2024, 2:08 a.m.