Shixiang Wang (王诗翔)
Shixiang Wang (王诗翔)
@kunstner Do you mean the signature exposure in each sample? If this is what you want, you can use {sigminer} package, which is compatible with {maftools}. The current version of...
@kunstner Yep! You can use `get_sig_similarity()` function. It is modified from source code of `maftools`, you can run `?sigminer::get_sig_similarity` in your R console to see the doc.
Recently, I uploaded sigminer package v1.0 to CRAN, and the per-sample exposure quantification has been documented in https://shixiangwang.gitee.io/sigminer-doc/sigfit.html. I hope it is helpful for related issues.
It takes a very long time after 100% prepare. My console is still busy, is it normal? Should add a notion for such case? ``` > library(TCGAbiolinks) > proj query...
I just found that the code below significantly slow the process. https://github.com/BioinformaticsFMRP/TCGAbiolinks/blob/6cd187eb10b27b260e16c7cb25216fdef919d43d/R/prepare.R#L1448-L1451 Instead, use `data.table` will speed up: ```r df = rbindlist(x, use.names = TRUE, idcol = "case_barcode") data.table::dcast(df, gene_id...
Check https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/493 may help.
I have same issue no matter I use conda vep or github vep when I test maf2maf ``` # vep install from bioconda perl maf2maf.pl --input-maf tests/test.maf --output-maf tests/test.vep.maf -vep-path...
Maybe you can use docker to create a Linux System to run all related commands or software. The vcf2maf can work for the latest VEP version. I use VEP 91...
sigprofiler里面还是使用的19个copy number signature