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constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
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why calling estimateSoup explicitly #28

Closed chansigit closed 4 years ago

chansigit commented 4 years ago

In the tutorial(https://cdn.rawgit.com/constantAmateur/SoupX/master/doc/pbmcTutorial.html), estimateSoup is called explicitly after constructing the SoupChannel.

sc = load10X(dataDirs, keepDroplets = TRUE)
sc = estimateSoup(sc)

but estimateSoup is actually called automatically in the following position https://github.com/constantAmateur/SoupX/blob/d7c58f74324d3f83b13e3a4a3e73e6c4426307b2/R/classFunctions.R#L35

Why should we call it explicitly again?

constantAmateur commented 4 years ago

You should not. This was included only to demonstrate what was being done automatically by the SoupChannel construction function.