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saezlab / decoupleR

R package to infer biological activities from omics data using a collection of methods.
https://saezlab.github.io/decoupleR/
GNU General Public License v3.0
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Differences between two ways of getting dorothea database #76

Closed yunbokai closed 1 year ago

yunbokai commented 1 year ago

Hi, It seems that I have two ways to get dorothea database. However, the result is different. First: data(dorothea_hs, package = "dorothea") network <- dorothea_hs confidence_lbls = c("A","B","C") network = network %>% dplyr::filter(confidence %in% confidence_lbls) Second: network <- get_dorothea(organism='human', levels=c('A', 'B', 'C')) Could you please explain the differences for me? The second way have more TFs. So is it the newest database? Thanks!

PauBadiaM commented 1 year ago

Hi @yunbokai

Thanks for checking out the package. Yes, this is because there are two versions, as discussed in #68 . We recommend using the one in decoupleR::get_dorothea as its the latest version.

yunbokai commented 1 year ago

Thanks a lot!