Dear all,

I do not understand on what depends the total signature contribution in the output of plotSamples() function. I would expect,
1/ either to have same level (1 for example) for each sample with a variation between signature contributions,
2/ or a correlation between total signature contribution and number of mutations per sample. On my dataset, the most mutated sample has the smallest total signature contribution and the less mutated sample has the second highest total signature contribution.
Could you explain on what depends the total signature contribution?

When a sample has a small total signature contribution, does it mean that it is not well explained by the determined signatures? In my dataset, the maximum total signature contribution I get for a sample is 0.06.

Thank you,
Jane

No clue for the representation of signature contribution?

To make the discussion more concrete... can you post a reproducible example?

Yes, here are more details. A reproducible example of my concern is not possible since I cannot send all my mutations to reconstruct the VRange object, but a figure should be clear.

I have 5 patients, for which I indicate the number of somatic SNV:

- ABA, 3244

- ALO, 20990

- ALS, 145

- CIA, 8589

- DJH, 10588

Above is the result of plotSamples(sigs_nmf) with 3 signatures obtained from NMF decomposition:

I do not understand how is computed the signature contribution and why the unit is so low (2, 4%).

What I you like to do is to plot the total number of mutations per sample and indicate how many are explained by each signature. Is it possible to get this information from one SomaticSignature function?

Thank you,

Jane

Sorry, my figure just disappeared when I submitted my answer. Is there a way to insert a graph here?