somaticInteractions {maftools} | R Documentation |
Performs Pair-wise Fisher's Exact test to detect mutually exclusive or co-occuring events. Also identifies gene sets mutated significantly.
somaticInteractions(maf, top = 25, genes = NULL, pvalue = c(0.05, 0.01), returnAll = FALSE, findPathways = TRUE, kMax = 3, fontSize = 0.8, verbose = TRUE)
maf |
|
top |
check for interactions among top 'n' number of genes. Defaults to top 25. |
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 |
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.
list of data.tables
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.
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools") laml <- read.maf(maf = laml.maf) somaticInteractions(maf = laml, top = 5)