Thanks for your excellent work! I am trying to apply your 30 biomarker score and driver gene activity modules on my T-ALL expression data, and I've read your code and paper carefully, it seems I still need some files (TARGET_TALL_merge.network.RData , Discovery_msTable.xlsx, and preTCR_dasatinib_Targets) to calculate the score and activity. I'll be grateful if you would like to share your output file, but I can totally understand if those data are under-protected.
To calculate driver activity, the TARGET TALL network ./SJAR/TARGET_TALL_merge.network.RData (source code) is the key file, and its upstream input file is sig_tf <- read.xlsx("SIG_TF_list.xlsx") (source code). I'm wondering if the same file between "SIG_TF_list.xlsx" and the default SIG and TF list in NetBID2 package?
To calculate 30 biomarker score in 3.1.get30biomarker_score.R, I think ./DATA/Discovery/Discovery_msTable.xlsx (source code) and ./DATA/combined/preTCR_dasatinib_Targets (no source code found) are necessary. I've checked the paper supplement data and only find some information at SourceData_Fig3C about preTCR_dasatinib_Targets, but I don't know if the list in source data is complete.
Thanks again and looking forward to your reply~
Best wishes
Bowen
xcxiongmao@126.com
Thanks for your excellent work! I am trying to apply your 30 biomarker score and driver gene activity modules on my T-ALL expression data, and I've read your code and paper carefully, it seems I still need some files (
TARGET_TALL_merge.network.RData
,Discovery_msTable.xlsx
, andpreTCR_dasatinib_Targets
) to calculate the score and activity. I'll be grateful if you would like to share your output file, but I can totally understand if those data are under-protected.To calculate driver activity, the TARGET TALL network
./SJAR/TARGET_TALL_merge.network.RData
(source code) is the key file, and its upstream input file issig_tf <- read.xlsx("SIG_TF_list.xlsx")
(source code). I'm wondering if the same file between "SIG_TF_list.xlsx" and the default SIG and TF list in NetBID2 package?To calculate 30 biomarker score in
3.1.get30biomarker_score.R
, I think./DATA/Discovery/Discovery_msTable.xlsx
(source code) and./DATA/combined/preTCR_dasatinib_Targets
(no source code found) are necessary. I've checked the paper supplement data and only find some information at SourceData_Fig3C aboutpreTCR_dasatinib_Targets
, but I don't know if the list in source data is complete.Thanks again and looking forward to your reply~ Best wishes Bowen xcxiongmao@126.com