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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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Error when using calcAUC (could not find function "matrixWrapper") #16

Closed justinesjw closed 6 years ago

justinesjw commented 6 years ago

Hi,

I have been following the tutorial on github and currently stuck in Step2_Regulons calcAUC() I've tried running it a few times using the code below:

motifs_AUC <- lapply(motifRankings, function(ranking) calcAUC(tfModules, ranking, aucMaxRank=0.01*nrow(ranking@rankings), nCores=12, verbose=FALSE))

but I seem to run into the same error

Error in matrixWrapper(matrix = aucMatrix, rowType = "gene-set", colType = "motif", : could not find function "matrixWrapper"

I'm running it on

Any idea on how can I fix this error?

Thanks, Justine

s-aibar commented 6 years ago

The current version of SCENIC (v0.1.6) requires AUCell 0.99.5. (Some functions were renamed on version 1.0). To correct the error, it should be enough with removing the current AUCell installation (remove.packages()) and running:

install.packages("http://scenic.aertslab.org/downloads/Rpackages/AUCell_0.99.5.tar.gz", repos=NULL)

Regards, Sara

justinesjw commented 6 years ago

Thanks for the speedy reply :+1: That solved the problem!

Thanks!!

yasin-chop commented 6 years ago

Hi, I have the same problem, but removing AUCell 1.0 and loading AUCell 0.99.5 did not solve the problem. I still get the same error. Do you have any idea about it? Thanks