I am working on mutation signatures from .maf files codes (https://github.com/mskcc/mutation-signatures)
using .maf file. At one stage where we calculate the confidence intervals and a quasi-pvalue for each signature I am face a complete blockage. I have tried my level best to understand my fault but failed. Since my knowledge in coding is limited I strongly believe that you guys will help me out in finding the fault in it.
The error: If I am running decomposition as mentioned in Readme file:
python main.py Stratton_signatures30.txt input.resamp.maf input.resamp.sig.txt
It shows me the following output only. (I am not sure is this what the output will be? if yes then what is its signifies?)
Sample Name Number of Mutations Signature.1 Signature.2 Signature.3 Signature.4 Signature.5 Signature.6 Signature.7 Signature.8 Signature.9 Signature.10 Signature.11 Signature.12 Signature.13 Signature.14 Signature.15 Signature.16 Signature.17 Signature.18 Signature.19 Signature.20 Signature.21 Signature.22 Signature.23 Signature.24 Signature.25 Signature.26 Signature.27 Signature.28 Signature.29 Signature.30
At the last step to calculate the (1 s.d.) confidence intervals and a quasi-pvalue for each signature: I used the following:
./sigsig_conf_int.R /input.resamp.sig.txt /home/output/input.resamp.sig.txt Finput.resamp.sig.conf_int.txt
Error in `[.data.table`(conf_int, , `:=`(c("Tumor_Sample_Barcode", "replicate"), : Supplied 2 columns to be assigned an empty list (which may be an empty data.table or data.frame since they are lists too). To delete multiple columns use NULL instead. To add multiple empty list columns, use list(list()). Calls: [ -> [.data.table In addition: Warning message: In `[.data.table`(conf_int, , `:=`(c("Tumor_Sample_Barcode", "replicate"), : with=FALSE ignored, it isn't needed when using :=. See ?':=' for examples. Execution halted
Please help me out, it would be of great help for me. I tried with all the available resources but exhausted. I am sure you will help me out.
I've had a lot of success with the deconstructSigs package in R for determining Stratton mutation signatures. You may want to try that one instead as it may be more user-friendly.