survGroup {maftools} | R Documentation

## Predict genesets associated with survival

### Description

Predict genesets associated with survival

### Usage

    survGroup(
      maf,
      top = 20,
      genes = NULL,
      geneSetSize = 2,
      minSamples = 5,
      clinicalData = NULL,
      time = "Time",
      Status = "Status",
      verbose = TRUE,
      plot = FALSE
    )

### Arguments

`maf` | an `MAF` object generated by `read.maf`
`top` | If genes is `NULL` by default used top 20 genes
`genes` | Manual set of genes
`geneSetSize` | Default 2
`minSamples` | minimum number of samples to be mutated to be considered for analysis. Default 5
`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.
`verbose` | Default TRUE
`plot` | Default FALSE If TRUE, generate KM plots of the genesets combinations.

### 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)
    survGroup(maf = laml, top = 20, geneSetSize = 1, time = "days_to_last_followup", Status = "Overall_Survival_Status", plot = FALSE)

[Package maftools version 2.10.05 Index]