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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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File 'int/1.4_GENIE3_linkList.Rds' does not exist #173

Closed EAC-T closed 2 years ago

EAC-T commented 3 years ago

Hello everyone,

I'm trying to run the tutorial on my data. I have a seurat object and I did this:

Get data from Seurat object:

exprMat<-GetAssayData(seurat, slot = "counts") exprMat<-as.matrix(exprMat) cellInfo <- data.frame(seuratCluster=Idents(seurat))

Initialize settings

scenicOptions <- initializeScenic(org="mgi", dbDir="C:/Users/name/Desktop/cisTarget_databases", nCores=10)

Co-expression network

genesKept <- geneFiltering(exprMat, scenicOptions) exprMat_filtered <- exprMat[genesKept, ] runCorrelation(exprMat_filtered, scenicOptions) exprMat_filtered_log <- log2(exprMat_filtered+1) runGenie3(exprMat_filtered_log, scenicOptions)

Finished running GENIE3

Build and score the GRN

exprMat_log <- log2(exprMat+1) scenicOptions@settings$dbs <- scenicOptions@settings$dbs["10kb"] scenicOptions <- runSCENIC_1_coexNetwork2modules(scenicOptions)

Error in .local(object, ...) : File 'int/1.4_GENIE3_linkList.Rds' does not exist.

I'm getting this error.

If I do: getInName(scenicOptions) I can see the genei3ll fileName "int/1.4_GENIE3_linkList.Rds"

Any help will be greatly appreciate it! Thank you

liaoshengyou commented 3 years ago

you shoud use the newst SCENIC version, read SCENIC_Running.html pipeline.