OncogenicPathways: Enrichment of known oncogenic pathways
In thesushantpatil/maftools: Summarize, Analyze and Visualize MAF Files
Description
Usage
Arguments
Details
Value
References
See Also
Examples
Description
Checks for enrichment of known oncogenic pathways
Usage
1
OncogenicPathways(maf, pathways = NULL, fontSize = 1, panelWidths = c(2, 4, 4))
Arguments
maf
an MAF object generated by read.maf
pathways
Can be a two column data.frame/tsv-file with genes and correspoding pathwaymappings. Default 'NULL', uses a predefined list of pathways. See reference for details.
fontSize
Default 1
panelWidths
Default c(2, 4, 4)
Details
Oncogenic signalling pathways are derived from TCGA cohorts. See reference for details.
Value
Prints fraction of altered pathway
References
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
See Also
Examples
1
2
3
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
OncogenicPathways(maf = laml)
thesushantpatil/maftools documentation built on May 18, 2020, 9:54 p.m.
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Description Usage Arguments Details Value References See Also Examples
Description
Checks for enrichment of known oncogenic pathways
Usage
1 | OncogenicPathways(maf, pathways = NULL, fontSize = 1, panelWidths = c(2, 4, 4))
|
Arguments
maf |
an |
pathways |
Can be a two column data.frame/tsv-file with genes and correspoding pathwaymappings. Default 'NULL', uses a predefined list of pathways. See reference for details. |
fontSize |
Default 1 |
panelWidths |
Default c(2, 4, 4) |
Details
Oncogenic signalling pathways are derived from TCGA cohorts. See reference for details.
Value
Prints fraction of altered pathway
References
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
See Also
Examples
1 2 3 | laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
OncogenicPathways(maf = laml)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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