question-mark

Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

Plot produce with sig. mutations at 0

See original GitHub issue

Issue Description

Hi,

We use SigProfiler in our cancer genome pipeline, on some sample decomposition verbose mode produce this output:

                                        ################ Sample 1 #################
############################# Initial Composition ####################################
   SBS1  SBS5  SBS96A
0   1.0   1.0   68.0
L2%:  0.055660557522576835
############################## Composition After Initial Remove ###############################
   SBS1  SBS5  SBS96C
0   0.0   0.0   70.0
L2%:  0.05906191827907873

Our sample match with SBS96C but figure produce contains graph for SBS1 and SBS5 this creates confusion. moreover, the number of sig. mutations signatures indicated is 0.

Code use to produce this figure:

    signatures = (
        output_dir
        + "SBS96/Suggested_Solution/De_Novo_Solution/De_Novo_Solution_Signatures_SBS96.txt"
    )
    activities = (
        output_dir
        + "SBS96/Suggested_Solution/De_Novo_Solution/De_Novo_Solution_Activities_SBS96.txt"
    )
    samples = output_dir + "SBS96/Samples.txt"
    output = output_dir + "Deconvolution_SB96_DeNovo"
    decomp.decompose(
        signatures, activities, samples, output, genome_build="GRCh38", verbose=True
    )

Issue Analytics

  • State:closed
  • Created a year ago
  • Comments:12

github_iconTop GitHub Comments

1reaction
mdbarnesUCSDcommented, Oct 15, 2021

We will be looking in the future to make updates to the decomposition module. We will look into modifying this behavior when we do so.

0reactions
oliverartzcommented, Jun 15, 2022

I have a similar question: I understand that SBS1 and SBS5 might appear in the decomposition plots although we have 0 mutations corresponding to those signatures. In that case, I would expect the contribution to the final signature to be 0%. I do, however, sometimes observe, that SBS1 or SBS5 contribute 0 mutations but around 2-3% to the final signature. Is there an explanation for that? Where do the 2-3% come from, if we have no mutations that contribute?

Thanks for your help and the development! Great tool!

Read more comments on GitHub >

github_iconTop Results From Across the Web

CoMutPlotter: a web tool for visual summary of mutations in ...
This summary plot can inspect gene mutation rate and sample mutation burden with their relevant clinical details, which is a common first step ......
Read more >
maftools : Summarize, Analyze and Visualize MAF Files
7.1 Plotting MAF summary. ... We can use plotmafSummary to plot the summary of the maf file, which displays number of variants in...
Read more >
Identification and validation of significant gene mutations to ...
The aim of our research is to identify significant gene mutations which can predict clinical benefit of immune checkpoint inhibitors in LUAD ...
Read more >
Rare Mutation Detection Best Practices Guidelines - Bio-Rad
Rare mutation detection (RMD) refers to detection of a sequence variant that is present at a very low frequency in a pool of...
Read more >
Mutational Signatures - COSMIC - Wellcome Sanger Institute
Different mutational processes generate unique combinations of mutation types, ... This summary includes the mutational profile, proposed aetiology and ...
Read more >

github_iconTop Related Medium Post

No results found

github_iconTop Related StackOverflow Question

No results found

github_iconTroubleshoot Live Code

Lightrun enables developers to add logs, metrics and snapshots to live code - no restarts or redeploys required.
Start Free

github_iconTop Related Reddit Thread

No results found

github_iconTop Related Hackernoon Post

No results found

github_iconTop Related Tweet

No results found

github_iconTop Related Dev.to Post

No results found

github_iconTop Related Hashnode Post

No results found