tcgaDriverBP: Compare genes to known TCGA drivers and their biological...

In maftools: Summarize, Analyze and Visualize MAF Files

Description

A small function which uses known cancer driver genes and their associatd pathways from TCGA cohorts. See reference for details

Usage

tcgaDriverBP(m, genes = NULL, top = 20, fontSize = 0.7)

Arguments

m	an MAF object
genes	genes to compare. Default 'NULL'.
top	Top number of genes to use. Mutually exclusive with 'genes' argument. Default 20
fontSize	Default 0.7

References

Bailey MH, Tokheim C, Porta-Pardo E, et al. Comprehensive Characterization of Cancer Driver Genes and Mutations . Cell. 2018;173(2):371–385.e18. doi:10.1016/j.cell.2018.02.060

Examples

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

Example output

-Reading
-Validating
-Silent variants: 475 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.379s elapsed (0.359s cpu) 
    Hugo_Symbol AlteredSamples pctAltered                   Pathway
 1:        FLT3             52     26.94%             RTK_signaling
 2:      DNMT3A             48     24.87% Epigenetics_DNA_modifiers
 3:        NPM1             33      17.1%           Chromatin_other
 4:        IDH2             20     10.36%                Metabolism
 5:        IDH1             18      9.33%                Metabolism
 6:        TET2             17      8.81%                      <NA>
 7:       RUNX1             16      8.29%      Transcription_factor
 8:        NRAS             15      7.77%            MAPK_signaling
 9:        TP53             15      7.77%          Genome_integrity
10:       CEBPA             13      6.74%                      <NA>
11:         WT1             12      6.22%      Transcription_factor
12:      PTPN11              9      4.66%           Other_signaling
13:       U2AF1              8      4.15%                  Splicing
14:         KIT              8      4.15%             RTK_signaling
15:        KRAS              8      4.15%            MAPK_signaling
16:        SMC3              7      3.63%                      <NA>
17:       SMC1A              6      3.11%          Genome_integrity
18:       STAG2              6      3.11%          Genome_integrity
19:        PHF6              6      3.11%                      <NA>
20:         TTN              6      3.11%                      <NA>
                                                                                                                               tcga_driver
 1:                                                                                                                                   LAML
 2:                                                                                                                       LAML,PANCAN,THCA
 3:                                                                                                                                   LAML
 4:                                                                                                                        LAML,LGG,PANCAN
 5:                                                                                                CHOL,GBM,LAML,LGG,LIHC,PANCAN,PRAD,SKCM
 6:                                                                                                                                   <NA>
 7:                                                                                                                       BRCA,LAML,PANCAN
 8:                                                                              BLCA,COADREAD,LGG,LIHC,OV,PANCAN,SKCM,TGCT,THCA,THYM,UCEC
 9: ACC,BLCA,BRCA,CESC,COADREAD,DLBC,ESCA,GBM,HNSC,KICH,KIRC,LAML,LGG,LIHC,LUAD,LUSC,MESO,OV,PAAD,PANCAN,PRAD,SARC,SKCM,STAD,THYM,UCEC,UCS
10:                                                                                                                                   <NA>
11:                                                                                                                            LAML,PANCAN
12:                                                                                                                        LAML,LGG,PANCAN
13:                                                                                                             LAML,LUAD,PAAD,PANCAN,UCEC
14:                                                                                                                  LAML,PANCAN,SKCM,TGCT
15:                                                BLCA,BRCA,CESC,COADREAD,KIRP,LAML,LIHC,LUAD,OV,PAAD,PANCAN,SKCM,STAD,TGCT,THCA,UCEC,UCS
16:                                                                                                                                   <NA>
17:                                                                                                                              LAML,UCEC
18:                                                                                                                        BLCA,GBM,PANCAN
19:                                                                                                                                   <NA>
20:                                                                                                                                   <NA>

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