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survGroup

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
)

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

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")
maftools

Summarize, Analyze and Visualize MAF Files

v2.6.05
MIT + file LICENSE
Authors
Anand Mayakonda [aut, cre] (<https://orcid.org/0000-0003-1162-687X>)
Initial release
2015-12-14

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