mafSurvGroup {maftools} | 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')

[Package maftools version 2.10.05 Index]