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evenrus / mmsig

A method for fitting a known mutational signature reference to mutational catalogues from cancer samples
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mm_fit_signatures Error #2

Closed parvathisudha closed 2 years ago

parvathisudha commented 2 years ago

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.