mafSurvGroup: Performs survival analysis for a geneset

In maftools: Summarize, Analyze and Visualize MAF Files

Description

Similar to mafSurvival but for a geneset

Usage

mafSurvGroup(
  maf,
  geneSet = NULL,
  clinicalData = NULL,
  time = "Time",
  Status = "Status"
)

Arguments

maf	an MAF object generated by read.maf
geneSet	gene names for which survival analysis needs to be performed. Samples with mutations in ALL of the genes provided are used as genes-set mutants.
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.

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)
mafSurvGroup(maf = laml, geneSet = c('DNMT3A', 'FLT3'), time = 'days_to_last_followup', Status = 'Overall_Survival_Status')

Example output

-Reading
-Validating
-Silent variants: 475 
-Summarizing
-Processing clinical data
-Finished in 0.484s elapsed (0.411s cpu) 
Looking for clinical data in annoatation slot of MAF..
Removed 11 samples with NA's
Median survival..
    Group medianTime   N
1: Mutant      242.5  18
2:     WT      379.5 164

maftools documentation built on Feb. 6, 2021, 2 a.m.