evenrus / mmsig Goto Github PK

Hi,

thank you very much for a great tool, which has proven very useful for our analyses!

I noticed that I got different results when running mmsig in the 2 modes, "vcf" and "classes" on the same samples. Upon looking into this in more detail, I figured that the reason was probably that the trinucleotide order returned by the function mut.to.sigs.input() (imported from deconstructSigs) returns the trinucleotides in a different order than my reference signature file. I solved this for myself by adjusting the order manually. However, it might be useful to include a consistency check in the code as well.

Many thanks, Verena

Hi everyone,

I am using mmsig for the detection of mutational signatures in a B-cell malignancy. I restricted my reference signatures to the most relevant signatures for this disease. However, I am having an issue when I plot the relative contribution of each sig per sample using plot_signatures. The plot script is not updating the new set of reference signatures, instead it is keeping the default from the example.

It is probably a simple issue to solve, but I have tried changing the names of the files and reinstalled the library.

I hope you can give a hint for solving this.

Many thanks,

Yurany

Hi,

I am trying to use music on the WGS data. My files were in hg38, and I lifted over to hg19.

I am getting an error: Error in if (sum(abs(alpha - old_alpha)) < 0.00001) { :
missing value where TRUE/FALSE needed

Command used :

sig_out <- mm_fit_signatures(muts.input=HT_SNVS_mmsig_hg19, 
                             sig.input=signature_ref,
                             input.format = "vcf",
                             sample.sigt.profs = NULL, 
                             strandbias = TRUE,
                             bootstrap = TRUE,
                             iterations = 100, # 1000 iterations recommended for stable results
                             refcheck=TRUE,
                             cos_sim_threshold = 0.01,
                             force_include = c("SBS13", "SBS-MM1"),
                             dbg=TRUE)

Error:
[1] "defaulting to use all signatures in the provided reference"
[1] "colnames sample.consigts.defn (before em)"
[1] "tri" "SBS1" "SBS2" "SBS5" "SBS8" "SBS9" "SBS13" "SBS18" "SBS35" "SBS84" "SBS-MM1"
Error in if (sum(abs(alpha - old_alpha)) < 0.00001) { :
missing value where TRUE/FALSE needed
In addition: Warning messages:

2: In lapply(X = X, FUN = FUN, ...) : NAs introduced by coercion

attached packages:
[1] mmsig_0.0.0.9000

Can you please help to solve this issue?

Thanks
Parvathi.