somaticInteractions: Exact tests to detect mutually exclusive, co-occuring and...

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

Exact tests to detect mutually exclusive, co-occuring and altered genesets.

Description

Performs Pair-wise Fisher's Exact test to detect mutually exclusive or co-occuring events.

Usage

somaticInteractions(
  maf,
  top = 25,
  genes = NULL,
  pvalue = c(0.05, 0.01),
  returnAll = TRUE,
  geneOrder = NULL,
  fontSize = 0.8,
  leftMar = 4,
  topMar = 4,
  showSigSymbols = TRUE,
  showCounts = FALSE,
  countStats = "all",
  countType = "all",
  countsFontSize = 0.8,
  countsFontColor = "black",
  colPal = "BrBG",
  revPal = FALSE,
  showSum = TRUE,
  plotPadj = FALSE,
  colNC = 9,
  nShiftSymbols = 5,
  sigSymbolsSize = 2,
  sigSymbolsFontSize = 0.9,
  pvSymbols = c(46, 42),
  limitColorBreaks = TRUE
)

Arguments

maf	an 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.
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
leftMar	Left margin. Default 4
topMar	Top margin. Default 4
showSigSymbols	Default TRUE. Heighlight significant pairs
showCounts	Default TRUE. Include number of events in the plot
countStats	Default 'all'. Can be 'all' or 'sig'
countType	Default 'cooccur'. Can be 'all', 'cooccur', 'mutexcl'
countsFontSize	Default 0.8
countsFontColor	Default 'black'
colPal	colPalBrewer palettes. See RColorBrewer::display.brewer.all() for details
revPal	Reverse the color palette. Default FALSE
showSum	show [sum] with gene names in plot, Default TRUE
plotPadj	Plot adj. p-values instead
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
sigSymbolsFontSize	size of font in legends
pvSymbols	vector of pch numbers for symbols of p-value for upper and lower thresholds c(upper, lower)
limitColorBreaks	limit color to extreme values. Default TRUE

Details

This function and plotting is inspired from genetic interaction analysis performed in the published study combining gene expression and mutation data in MDS. See reference for details.

Value

list of data.tables

References

Gerstung M, Pellagatti A, Malcovati L, et al. Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes. Nature Communications. 2015;6:5901. doi:10.1038/ncomms6901.

Examples

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
somaticInteractions(maf = laml, top = 5)

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