somaticInteractions - co-occurrence data not adding up

[kernyu]

Describe the issue
I have a gene barplot of what genes are frequently seen as a co-variant with a gene of choice (DNMT3A).

However, when I plot co-occurrence using somaticInteractions in maftools, I find that the genes that co-occur frequently with DNMT3A are seen as slightly mutually exclusive, so I'm trying to understand how co-occurrences are calculated.

Command
Please post your commands and the output (errors or any unexpected output)

somaticInteractions(vaf001.merged.maf, top = 5, pvalue = c(0.05, 0.1))

Session info
Run sessionInfo() and post the output below

[PoisonAlien]

Hi,

The best way is to draw an oncoplot for these 5 genes and check the pattern.