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View Code? Open in Web Editor NEWA method for fitting a known mutational signature reference to mutational catalogues from cancer samples
License: Other
A method for fitting a known mutational signature reference to mutational catalogues from cancer samples
License: Other
Hi,
I am trying to use mmsig 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.
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 mmsig on the WGS data. My files are in hg38.
I am using COSMIC (v3.2) GRCh38 SBS as the reference file. I have also set refcheck = FALSE. Even then, few snvs are not recognized by the program.
Code:
smm_sig_outhg38 <- mm_fit_signatures(muts.input=snvs, sig.input=sig_ref_hg38, input.format = "vcf", sample.sigt.profs = NULL, strandbias = FALSE, bootstrap = TRUE, iterations = 20, refcheck=FALSE, cos_sim_threshold = 0.01, force_include = c("SBS13","SBS2"), dbg=TRUE)
Error:
Error in .Call2("C_solve_user_SEW", refwidths, start, end, width, translate.negative.coord, : solving row 36159: 'allow.nonnarrowing' is FALSE and the supplied start (78180144) is > refwidth + 1
Do you recommend to change any other parameters here while running the program for hg38 reference?
Thanks!
Parvathi.
Hello, I am trying to use the mmsig example from the README but using all reference signatures. It hasn't finished this short example in the past hour, my guess is that it may be in an endless while loop. Any thoughts? Below is the code I ran:
library(mmsig)
library(MutationalPatterns)
data(mm_5_col)
data(signature_ref)
#Get known signatures
data(signature_ref)
signatures = get_known_signatures()
all_sigs <- cbind(signature_ref[c("sub","tri")],signatures)
sig_out <- mm_fit_signatures(muts.input=mm_5_col_subset[1:50,],
sig.input=all_sigs,
input.format = "vcf",
sample.sigt.profs = NULL,
strandbias = TRUE,
bootstrap = TRUE,
iterations = 20, # 1000 iterations recommended for stable results
refcheck=TRUE,
cos_sim_threshold = 0.01,
dbg=FALSE)
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
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