getGeneSummary: extract gene summary from MAF or GISTIC object

In maftools: Summarize, Analyze and Visualize MAF Files

Description

extract gene summary from MAF or GISTIC object

Usage

getGeneSummary(x)

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

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

Arguments

x	An object of class MAF or GISTIC

Value

gene summary table

Examples

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

Example output

-Reading
-Validating
-Silent variants: 475 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.458s elapsed (0.433s cpu) 
      Hugo_Symbol Frame_Shift_Del Frame_Shift_Ins In_Frame_Del In_Frame_Ins
   1:        FLT3               0               0            1           33
   2:      DNMT3A               4               0            0            0
   3:        NPM1               0              33            0            0
   4:        IDH2               0               0            0            0
   5:        IDH1               0               0            0            0
  ---                                                                      
1237:      ZNF689               0               0            0            0
1238:      ZNF75D               0               0            0            0
1239:      ZNF827               1               0            0            0
1240:       ZNF99               0               0            0            0
1241:        ZPBP               0               0            0            0
      Missense_Mutation Nonsense_Mutation Splice_Site total MutatedSamples
   1:                15                 0           3    52             52
   2:                39                 5           6    54             48
   3:                 1                 0           0    34             33
   4:                20                 0           0    20             20
   5:                18                 0           0    18             18
  ---                                                                     
1237:                 1                 0           0     1              1
1238:                 1                 0           0     1              1
1239:                 0                 0           0     1              1
1240:                 1                 0           0     1              1
1241:                 1                 0           0     1              1
      AlteredSamples
   1:             52
   2:             48
   3:             33
   4:             20
   5:             18
  ---               
1237:              1
1238:              1
1239:              1
1240:              1
1241:              1

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