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. Also identifies gene sets mutated significantly.

### Usage

    somaticInteractions(maf, top = 25, genes = NULL, pvalue = c(0.05,
      0.01), returnAll = FALSE, geneOrder = NULL, findPathways = TRUE,
      kMax = 3, fontSize = 0.8, verbose = 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.
`findPathways` | Uses all mutually exclusive set of genes to further identify altered pathways. Default TRUE
`kMax` | Default 3. maximum gene set size if findPathways is TRUE. This is time consuming for > 3.
`fontSize` | cex for gene names. Default 0.8
`verbose` | 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 2.0.16 Index]