somaticInteractions {maftools} | R Documentation

## 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,
      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` | 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
`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
`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
`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)

[Package maftools version 2.10.05 Index]