getSampleSummary: extract sample summary from MAF or GISTIC object

In maftools: Summarize, Analyze and Visualize MAF Files

Description

extract sample summary from MAF or GISTIC object

Usage

getSampleSummary(x)

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

## S4 method for signature 'GISTIC'
getSampleSummary(x)

Arguments

x	An object of class MAF or GISTIC

Value

sample summary table

Examples

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

Example output

-Reading
-Validating
-Silent variants: 475 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.525s elapsed (0.491s cpu) 
     Tumor_Sample_Barcode Frame_Shift_Del Frame_Shift_Ins In_Frame_Del
  1:         TCGA-AB-3009               0               5            0
  2:         TCGA-AB-2807               1               0            1
  3:         TCGA-AB-2959               0               0            0
  4:         TCGA-AB-3002               0               0            0
  5:         TCGA-AB-2849               0               1            0
 ---                                                                  
189:         TCGA-AB-2942               0               0            0
190:         TCGA-AB-2946               0               0            0
191:         TCGA-AB-2954               0               0            0
192:         TCGA-AB-2982               0               0            0
193:         TCGA-AB-2903               0               0            0
     In_Frame_Ins Missense_Mutation Nonsense_Mutation Splice_Site total
  1:            1                25                 2           1    34
  2:            0                16                 3           4    25
  3:            0                22                 0           1    23
  4:            0                15                 1           5    21
  5:            0                16                 1           2    20
 ---                                                                   
189:            1                 0                 0           0     1
190:            0                 1                 0           0     1
191:            0                 1                 0           0     1
192:            0                 1                 0           0     1
193:            0                 0                 0           0     0

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