Error in inferNonExpressedGenes(scl) : could not find function "inferNonExpressedGenes"

constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

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Error in inferNonExpressedGenes(scl) : could not find function "inferNonExpressedGenes" #20

Closed molybdenumt closed 4 years ago

molybdenumt commented 4 years ago

I keep getting the error: Error in inferNonExpressedGenes(scl) : could not find function "inferNonExpressedGenes" But when I pull up the help document, using "?inferNonExpressedGenes" it shows the document.

I tried the function in R version 3.5.1 and R version 3.6.1. I'm not sure what is going on.

constantAmateur commented 4 years ago

The inferNonExpressed genes should no longer be directly called by the user and is not provided to the user, that is why you are getting a message that it could not be found.

I decided to remove it because people were misusing it as an automated gene detection function, when it was intended as a heuristic. As you have noticed, the help file is still available.

molybdenumt commented 4 years ago

What is the function to replace it? I'm trying to figure out which genes to use as soup. It would be good to be able to get the expression level of genes and then I can consider which genes to use as soup.

constantAmateur commented 4 years ago

The vignette shows how to look at the most expressed genes in the background head(sc$soupProfile[order(sc$soupProfile$est, decreasing = TRUE), ], n = 20)

But these are not necessarily the most useful. The plotMarkerDistribution function will show a suggestion of 20 potentially useful genes when run without specifying geneSets. But it is up to you to pick something useful to your use case.