mafSurvGroup: Performs survival analysis for a geneset
In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

mafSurvGroup

R Documentation

Performs survival analysis for a geneset

Description

Similar to mafSurvival but for a geneset

Usage

mafSurvGroup(
  maf,
  geneSet = NULL,
  minMut = NA,
  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.
`minMut`	minimum number of mutated genes in the 'geneSet' to consider a sample as a mutant. Default, 'NA', samples with all the genes mutated are treated as mutant group.
`clinicalData`	`dataframe` containing events and time to events. Default looks for clinical data in annotation slot of `MAF`.
`time`	column name containing 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')

PoisonAlien/maftools documentation built on April 7, 2024, 2:49 a.m.