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, 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.

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 1.8.0 Index]