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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What's goal dividing the original gene list into nParts pieces #41

Closed eleozzr closed 6 years ago

eleozzr commented 6 years ago

What's the function of parameter nParts in runGenie3 function. In practice, how we specify the nParts.

SCENIC/R/runGenie3.R, line 30

genesSplit <- split(sort(rownames(exprMat)), 1:nParts) and I don't understand why you use sort? Shouldn't we put all genes together to infer gene regulatory networks from gene expression data??

s-aibar commented 6 years ago

Hello,

Yes, all genes are used to infer the regulatory networks, but each gene can be calculated individually. Since it big datasets it can take several hours/days to run GENIE3 for all the genes, the execution is split into pieces to avoid the loss of the full run in case it is interrupted. This is not required, but rather a workaround for those users that cannot/do not want to use GRNBoost (the recommended method).