discoversomaticInteractions: discoversomaticInteractions
In Rediscover: Identify Mutually Exclusive Mutations

discoversomaticInteractions

R Documentation

discoversomaticInteractions

Description

Function adapted to maftools where given a .maf file, it graphs the somatic interactions between a group of genes, i.e., the combination of gene expression and mutation data to detect mutually exclusive or co-ocurring events.

Usage

discoversomaticInteractions(
  maf,
  top = 25,
  genes = NULL,
  pvalue = c(0.05, 0.01),
  getMutexMethod = "ShiftedBinomial",
  getMutexMixed = TRUE,
  returnAll = TRUE,
  geneOrder = NULL,
  fontSize = 0.8,
  showSigSymbols = TRUE,
  showCounts = FALSE,
  countStats = "all",
  countType = "all",
  countsFontSize = 0.8,
  countsFontColor = "black",
  colPal = "BrBG",
  showSum = TRUE,
  colNC = 9,
  nShiftSymbols = 5,
  sigSymbolsSize = 2,
  sigSymbolsFontSize = 0.9,
  pvSymbols = c(46, 42),
  limitColorBreaks = TRUE
)

Arguments

`maf`	maf object generated by read.maf
`top`	check for interactions among top 'n' number of genes. Defaults to top 25. genes
`genes`	List of genes among which interactions should be tested. If not provided, test will be performed between top 25 genes.
`pvalue`	Default c(0.05, 0.01) p-value threshold. You can provide two values for upper and lower threshold.
`getMutexMethod`	Method for the 'getMutex' function (by default "ShiftedBinomial")
`getMutexMixed`	Mixed parameter for the 'getMutex' function (by default TRUE)
`returnAll`	If TRUE returns test statistics for all pair of tested genes. Default FALSE, returns for only genes below pvalue threshold.
`geneOrder`	Plot the results in given order. Default NULL.
`fontSize`	cex for gene names. Default 0.8
`showSigSymbols`	Default TRUE. Heighlight significant pairs
`showCounts`	Default FALSE. Include number of events in the plot
`countStats`	Default 'all'. Can be 'all' or 'sig'
`countType`	Default 'all'. Can be 'all', 'cooccur', 'mutexcl'
`countsFontSize`	Default 0.8
`countsFontColor`	Default 'black'
`colPal`	colPalBrewer palettes. Default 'BrBG'. See RColorBrewer::display.brewer.all() for details
`showSum`	show [sum] with gene names in plot, Default TRUE
`colNC`	Number of different colors in the palette, minimum 3, default 9
`nShiftSymbols`	shift if positive shift SigSymbols by n to the left, default 5
`sigSymbolsSize`	size of symbols in the matrix and in legend. Default 2
`sigSymbolsFontSize`	size of font in legends. Default 0.9
`pvSymbols`	vector of pch numbers for symbols of p-value for upper and lower thresholds c(upper, lower). Default c(46, 42)
`limitColorBreaks`	limit color to extreme values. Default TRUE

Details

Internally, this function run the getMutex function. With the 'getMutexMethod' parameter user might select the 'method' parameter of the getMutex function. For more details run '?getMutex'

#' @return A list of data.tables and it will print a heatmap with the results.

References

Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. 2018. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Research. http://dx.doi.org/10.1101/gr.239244.118

Examples


## Not run: 

  #An example of how to perform the function,
  #using data from TCGA, Colon Adenocarcinoma in this case. 
  
  #coad.maf <- GDCquery_Maf("COAD", pipelines = "muse") %>% read.maf
  coad.maf <- read.maf(GDCquery_Maf("COAD", pipelines = "muse"))
  discoversomaticInteractions(maf = coad.maf, top = 35, pvalue = c(1e-2, 2e-3))
  
## End(Not run)

Rediscover documentation built on April 14, 2023, 5:14 p.m.