comet_exact_test r function fails with 0 inclusive counts.
Opened this issue · 2 comments
PoisonAlien commented
comet_exact_test()
fails to run when number of co-occurring samples is zero during 2^2 contingency table.
For example, In TCGA LAML, NPM1 and RUNX1 show strong mutually exclusiveness. Following is the table for NPM1 and RUNX1:
binaryString | number |
---|---|
00 | 124 |
01 | 54 |
10 | 18 |
11 | 0 |
> comet_exact_test(tbl = c(124, 54, 18, 0))
Error in `[<-`(`*tmp*`, , col_index, value = c(1L, 1L)) :
subscript out of bounds
But code runs without error if I replace last entry with 1.
> comet_exact_test(tbl = c(124, 54, 18, 1))
[1] 0.00720818
So is it necessary for two genes to have at least one common sample to run comet ?
Thanks.
P.S: Sorry if this is not the right place to ask this.
bournewu commented
Thank you for your interest in our software.
It is a bug when plotting mutation matrix if no co-occurrence occur. We will fix this asap.
If you need only the p-value, try disable the plot function by using the following code:
comet_exact_test(c(124,18,18,0) , mutmatplot=F)
PoisonAlien commented
I should have tried this before asking.
Thank you.