OncogenicPathways: Enrichment of known oncogenic pathways
In maftools: Summarize, Analyze and Visualize MAF Files

Description Usage Arguments Details Value References See Also Examples

Checks for enrichment of known oncogenic pathways

1	OncogenicPathways(maf, pathways = NULL, fontSize = 1, panelWidths = c(2, 4, 4))

`maf`	an `MAF` object generated by `read.maf`
`pathways`	Can be a two column data.frame/tsv-file with pathway-name and genes involved in them. Default 'NULL', uses a predefined list of pathways. See reference for details.
`fontSize`	Default 1
`panelWidths`	Default c(2, 4, 4)

Oncogenic signalling pathways are derived from TCGA cohorts. See reference for details.

Prints fraction of altered pathway

Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S et al. 2018. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell 173: 321-337 e310

PlotOncogenicPathways

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

-Reading
-Validating
-Silent variants: 475 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.410s elapsed (0.368s cpu) 
   Pathway  N n_affected_genes fraction_affected Mutated_samples
1:    PI3K 29                1        0.03448276               1
2:    NRF2  3                1        0.33333333               1
3:    TP53  6                2        0.33333333              15
4:     WNT 68                3        0.04411765               4
5:     MYC 13                3        0.23076923               3
6:   NOTCH 71                6        0.08450704               8
7:   Hippo 38                7        0.18421053               7
8: RTK-RAS 85               18        0.21176471              97
   Fraction_mutated_samples
1:              0.005181347
2:              0.005181347
3:              0.077720207
4:              0.020725389
5:              0.015544041
6:              0.041450777
7:              0.036269430
8:              0.502590674