mut.to.sigs.input for DBS signatures creates empty output

[kittysher]

Hi
I am trying to analyse double base substitution (DBS) signatures using the deconstruct sigs R package. I have run the example code below with success:
sigs.input = mut.to.sigs.input(mut.ref = sample.mut.ref, sample.id = "Sample", chr = "chr", pos = "pos", ref = "ref", alt = "alt", bsg = BSgenome.Hsapiens.UCSC.hg19, sig.type = 'DBS', dbs_table = dbs_possible)

However when I try to run this on my own data, I get a completely empty output. My data is in the same format with the same column names and data types per column. No errors come up just the output is empty. The only other thing I have to change is the reference genome as my data uses hg38.

When I change the sig.type to SBS with my data, this works fine. So it is something specifically wrong with the DBS part.

Any suggestions would be really helpful!

Thanks, Kitty

[raerose01]

Hi Kitty, could you try again with the most recent version on Github? I think I may have fixed this. Otherwise, could you send an example file that re-creates the error?

Thanks,

Rachel

[kittysher]

demo_github_file.txt
Hi Rachel,

I have had a go with the newest package version but I'm still having the same issue as before where the DBS produces an empty output but it works for sig type SBS. I've attached the file I'm using for you to see.

Thanks for your help,
Kitty

[kvaldez]

Hi Rachel,

I'm having also having this issue. I attached my input data and I am using the command below:

sigs.input <- mut.to.sigs.input(mut.ref = mut_data, sample.id = "Sample", chr = "Chr", pos = "Start", ref = "Ref", alt = "Alt", sig.type = 'DBS', dbs_table = dbs_possible)

git.txt

Should my input data include doublet substitutions?

Thanks in advance for any assistance!

Kristin

[raerose01]

Hi Kristin,

Is the file you attached the one you are working with? It doesn't look like there are any DBS (e.g. CC>TT) in there.

Let me know if you have another file, or if I've missed them.

Best,

Rachel

[kvaldez]

Hi Rachel,

Thanks I was wondering if we'd need this in our input or if it was somehow inferred. I'll have to see if there's a way to output DBS from our pipeline.

Thanks again,
Kristin