mafSurvival: Performs survival analysis

In thesushantpatil/maftools: Summarize, Analyze and Visualize MAF Files

Description

Performs survival analysis by grouping samples from maf based on mutation status of given gene(s) or manual grouping of samples.

Usage

mafSurvival(
  maf,
  genes = NULL,
  samples = NULL,
  clinicalData = NULL,
  time = "Time",
  Status = "Status",
  groupNames = c("Mutant", "WT"),
  showConfInt = TRUE,
  addInfo = TRUE,
  col = c("maroon", "royalblue"),
  isTCGA = FALSE,
  textSize = 12,
  fn = NULL,
  width = 6,
  height = 6
)

Arguments

maf	an MAF object generated by read.maf
genes	gene names for which survival analysis needs to be performed. Samples with mutations in any one of the genes provided are used as mutants.
samples	samples to group by. Genes and samples are mutually exclusive.
clinicalData	dataframe containing events and time to events. Default looks for clinical data in annotation slot of MAF.
time	column name contining time in clinicalData
Status	column name containing status of patients in clinicalData. must be logical or numeric. e.g, TRUE or FALSE, 1 or 0.
groupNames	names for groups. Should be of length two. Default c("Mutant", "WT")
showConfInt	TRUE. Whether to show confidence interval in KM plot.
addInfo	TRUE. Whether to show survival info in the plot.
col	colors for plotting.
isTCGA	FALSE. Is data is from TCGA.
textSize	Text size for surv table. Default 7.
fn	NULL. If provided saves pdf plot with basename fn.
width	width of plot to be saved. Default 6
height	height of plot to be saved. Default 6

Details

This function takes MAF file and groups them based on mutation status associated with given gene(s) and performs survival analysis. Requires dataframe containing survival status and time to event. Make sure sample names match to Tumor Sample Barcodes from MAF file.

Value

Survival plot

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml.clin <- system.file("extdata", "tcga_laml_annot.tsv", package = "maftools")
laml <- read.maf(maf = laml.maf,  clinicalData = laml.clin)
mafSurvival(maf = laml, genes = 'DNMT3A', time = 'days_to_last_followup', Status = 'Overall_Survival_Status', isTCGA = TRUE)

thesushantpatil/maftools documentation built on May 18, 2020, 9:54 p.m.