pathways: Enrichment of known oncogenic or custom pathways

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

Enrichment of known oncogenic or custom pathways

Description

Checks for enrichment of known or custom pathways

Usage

pathways(
  maf,
  pathdb = "sigpw",
  pathways = NULL,
  fontSize = 1,
  panelWidths = c(2, 4, 4),
  plotType = NA,
  col = "#f39c12"
)

Arguments

maf	an MAF object generated by read.maf
pathdb	Either 'sigpw' or 'smgbp', 'sigpw' uses known oncogenic signalling pathways (Sanchez/Vega et al) whereas 'smgbp' uses pan cancer significantly mutated genes classified according to biological process (Bailey et al). Default smgbp
pathways	Can be a two column data.frame/tsv-file with gene names and pathway-name involved in them. Default 'NULL'. This argument is mutually exclusive with pathdb
fontSize	Default 1
panelWidths	Default c(2, 4, 4)
plotType	Can be 'treemap' or 'bar'. Set NA to suppress plotting. Default NA
col	Default #f39c12

Details

Oncogenic signalling and SMG pathways are derived from TCGA cohorts. See references for details.

Value

fraction of altered pathway. attr genes contain pathway contents

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 Bailey, Matthew H et al. “Comprehensive Characterization of Cancer Driver Genes and Mutations.” Cell vol. 173,2 (2018): 371-385.e18.

See Also

plotPathways

Examples

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

PoisonAlien/maftools documentation built on Nov. 10, 2024, 6:01 p.m.