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FloWuenne / scFunctions

Functions for single cell data analysis
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Error in calculate_rrs #3

Open ShaowenJ opened 4 years ago

ShaowenJ commented 4 years ago

Hi scFunctions Developer,

Nice package for doing this. But in the tutorial, I think you missed the code for calculating the RSS. Nevertheless, I got an error while I tried to do that: rrs_df <- calculate_rrs(cellInfo,binary_regulons, cell_type_column = "seuratCluster")

Error in binary_regulons[regulon, ] : incorrect number of dimensions

cellInfo is the metadata table from seurat

Thanks!

GildasLepennetier commented 4 years ago

Do you actually have rownames in your binary_regulons?

FloWuenne commented 4 years ago

Hi @Lesdormis,

sorry for the very let reply! You are totally right and I did forget to put the code for calculating the rrs. I will add this very soon and add a very short tutorial on how to process results from the new SCENIC nextflow pipeline, as this makes it much easier to produce SCENIC results from single-cell data than the R implementation:

In the meantime, you can check out: SCENICprotocol

and this notebook where they also calculate rrs: https://github.com/aertslab/SCENICprotocol/blob/master/notebooks/PBMC10k_downstream-analysis.ipynb