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

Description Usage Arguments Value Examples

Similar to mafSurvival but for a geneset

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

`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.

Survival plot

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')