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ShixiangWang / sigminer

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html
https://shixiangwang.github.io/sigminer/
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get_sig_similarity(mt_sig) error #337

Closed tangwei1129 closed 3 years ago

tangwei1129 commented 3 years ago

Hi sigminer developer, I tried to follow the tutorial of the sigminer in the github, and had an error when I used get_sig_similarity(mt_sig).

sim <- get_sig_similarity(mt_sig) Error in get_sig_similarity(mt_sig) : The following components cannot be found in reference! A[C>A]A A[C>A]C A[C>A]G A[C>A]T A[C>G]A A[C>G]C A[C>G]G A[C>G]T A[C>T]A A[C>T]C A[C>T]G A[C>T]T A[T>A]A A[T>A]C A[T>A]G A[T>A]T A[T>C]A A[T>C]C A[T>C]G A[T>C]T A[T>G]A A[T>G]C A[T>G]G A[T>G]T C[C>A]A C[C>A]C C[C>A]G C[C>A]T C[C>G]A C[C>G]C C[C>G]G C[C>G]T C[C>T]A C[C>T]C C[C>T]G C[C>T]T C[T>A]A C[T>A]C C[T>A]G C[T>A]T C[T>C]A C[T>C]C C[T>C]G C[T>C]T C[T>G]A C[T>G]C C[T>G]G C[T>G]T G[C>A]A G[C>A]C G[C>A]G G[C>A]T G[C>G]A G[C>G]C G[C>G]G G[C>G]T G[C>T]A G[C>T]C G[C>T]G G[C>T]T G[T>A]A G[T>A]C G[T>A]G G[T>A]T G[T>C]A G[T>C]C G[T>C]G G[T>C]T G[T>G]A G[T>G]C G[T>G]G G[T>G]T T[C>A]A T[C>A]C T[C>A]G T[C>A]T T[C>G]A T[C>G]C T[C>G]G T[C>G]T T[C>T]A T[C>T]C T[C>T]G T[C>T]T T[T>A]A T[T>A]C T[T>A]G T[T>A]T T[T>C]A T[T>C]C T[T>C]G T[T>C]T T[T>G]A T[T>G]C T[T>G]G T[T>G]T NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

then I checked the mt_sig

sig_signature(mt_sig) Sig1 Sig2 Sig3 Sig4 Sig5 Sig6 Sig7 T:A[T>C]A 1.157634e-15 1.946577e-02 2.008333e-02 8.971821e-03 8.323871e-04 1.037767e-20 2.174382e-03 U:A[T>C]A 1.570167e-15 3.085610e-03 1.300561e-02 6.112988e-03 3.582062e-12 3.191147e-18 7.558961e-03 B:A[T>C]A 4.154526e-16 6.281431e-15 7.125082e-16 2.772421e-03 1.623875e-13 8.705931e-15 7.576711e-10 N:A[T>C]A 9.379825e-16 1.855438e-14 9.143889e-15 5.168096e-15 2.872419e-15 3.666839e-14 7.239519e-15 T:C[T>C]A 5.071049e-04 4.246512e-03 4.682144e-03 9.433469e-21 2.756027e-03 1.037767e-20 2.510236e-03 U:C[T>C]A 4.574777e-04 3.429800e-03 1.355851e-03 7.376664e-03 1.006630e-03 3.097024e-03 4.600730e-04 B:C[T>C]A 5.756015e-16 6.602645e-04 1.302937e-15 2.358308e-04 2.509056e-15 1.219123e-14 1.163049e-20 N:C[T>C]A 9.379825e-16 1.855438e-14 9.143889e-15 5.168096e-15 2.872419e-15 3.666839e-14 7.239519e-15 T:G[T>C]A 1.107974e-03 4.474565e-03 5.695898e-03 8.924056e-04 5.189459e-03 1.037767e-20 3.635121e-03 U:G[T>C]A 2.621411e-04 9.605980e-21 8.526817e-03 2.991077e-03 2.706746e-03 7.714915e-04 1.163049e-20 B:G[T>C]A 4.228335e-16 3.063935e-15 7.618479e-04 5.964313e-04 1.106248e-14 3.172285e-14 1.163049e-20 . . . . all the 96 patterns had additional 4 categories with T,U,B,N, and that causes the error for get_sig_similarity. do you have any idea how to fix it? Thank you very much!

Wei NCI/NIH

ShixiangWang commented 3 years ago

The matrix you passing for extraction is not correct，please take a look at the input of sig_extract

tangwei1129 commented 3 years ago

Thank you for your reply. i found if i turned off 'add_trans_bias = F' in sig_tally, it works out with the right header when getting nmf.matrix. so i want to use 'add_trans_bias =T', which category of T/U/B/N should I use for the further analysis? and how should I process to the next step?

ShixiangWang commented 3 years ago

Subset the T/U

ShixiangWang commented 3 years ago

I update the code and return 192 classes at default, try installing from github

tangwei1129 commented 3 years ago

it works. thank you.

ShixiangWang commented 3 years ago

You are welcome