getClinicalData: extract annotations from MAF object

In maftools: Summarize, Analyze and Visualize MAF Files

Description

extract annotations from MAF object

Usage

getClinicalData(x)

## S4 method for signature 'MAF'
getClinicalData(x)

Arguments

x	An object of class MAF

Value

annotations associated with samples in MAF

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
getClinicalData(x = laml)

Example output

-Reading
-Validating
-Silent variants: 475 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.694s elapsed (0.543s cpu) 
     Tumor_Sample_Barcode
  1:         TCGA-AB-2802
  2:         TCGA-AB-2803
  3:         TCGA-AB-2804
  4:         TCGA-AB-2805
  5:         TCGA-AB-2806
 ---                     
189:         TCGA-AB-3007
190:         TCGA-AB-3008
191:         TCGA-AB-3009
192:         TCGA-AB-3011
193:         TCGA-AB-3012

maftools documentation built on Feb. 6, 2021, 2 a.m.