error in strsplit when plot "coOncoplot" about maftools

[PoisonAlien]

Hi,

Can you send me a sample file so that I can see whats going on. You can change barcodes and other details.

[shirleydaidai]

I found the error might be due to no mutations in one of the compared MAF.

print(pt.vs.rt)
$results
Hugo_Symbol male female pval or ci.up ci.low
1: USH2A 11 0 0.000771904 Inf 2.4659925 Inf
2: ASXL3 9 0 0.003384388 Inf 1.8599523 Inf
3: ARID1A 8 0 0.007011792 Inf 1.5771181 Inf
4: DCHS1 8 0 0.007011792 Inf 1.5771181 Inf
5: FMN2 8 0 0.007011792 Inf 1.5771181 Inf

---

[shirleydaidai]

Well. I finally got the answer. There must be at least 2 mutations in one of the compared MAF to plot coOncoplot

[PoisonAlien]

Hi,
Its not supposed to be the case. It should still draw the plot even when mutations are missing in one of the sample (take a look at the example in vignette, RARA has no mutation). i think this an issue with factor to character conversion.

Sorry I have a test tomorrow and won't be able to fix it soon. I will work on this over the weekend. Meanwhile can you write those two maf (male and female) to output files (write.mafSummary function) and then read them separately and try to plot and see if it works?

[shirleydaidai]

I have outputted 2 files and re-readed in. But this error exists:

Error in strsplit(x = variant.classes, split = ";", fixed = TRUE) : 
  non-character argument

[PoisonAlien]

Hi,
Can you share your samples files ?

[PoisonAlien]

Hi,

I see the issue here, female have no mutations for these genes at all ! So no way to plot them, maybe you include a gene which is mutated in at least one sample among female ? Anyways I have made a temporary fix. You can pull it from github. Target devel brach.

devtools::install_github(repo = "PoisonAlien/maftools", ref = 'devel')

P.S: I have deleted your shared link, very interesting data.

[shirleydaidai]

Thank you!