Rediscover (version 0.3.3)

discoversomaticInteractions: 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

# \donttest{
if (FALSE) {

  #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))
  }

# }