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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, 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 in get_regulonsAuc(loom) : The argument 'attrName' is not available in this loom file. Possible values include: RegulonsAUC. #195

Closed charlesgwellem closed 4 years ago

charlesgwellem commented 4 years ago

Can any one help me with a hint why I cannot read fully in output from pySCENIC in to Rstudio? I used pyCENIC to run the SCENIC workflow and I used the following command

(base) charles@rahul-SYS-7039A-I:~/Downloads/ssc_Valenzi$ sudo ./nextflow run aertslab/SCENICprotocol -profile docker --loom_input ssc_ECs_Valenzi.loom --loom_outputhttps://github.com/aertslab/pySCENIC/issues/194 pyscenic_integrated-output.loom --TFs hs_hgnc_curated_tfs.txt --motifs motifs-v9-nr.hgnc-m0.001-o0.0.tbl --db hg38__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.feather --thr_min_genes 1 --threads 26

But I want to read in results about the regulons in R. So I

pyScenicLoomFile <- file.path(getwd(), "pyscenic_integrated-output.loom")
loom <- open_loom(pyScenicLoomFile, mode="r")

# Regulon AUC and thresholds
regulonsAUC <- get_regulonsAuc(loom)

But I got the error

Error in get_regulonsAuc(loom) : 
  The argument 'attrName' is not available in this loom file. Possible values include: RegulonsAUC.

Thanks in advance for your kind help.

cflerin commented 4 years ago

Hi @charlesgwellem ,

This is a SCopeLoomR issue, it seems. The default value for the attrName was recently changed. Try:

regulonsAUC <- get_regulonsAuc(loom, attrName="RegulonsAUC")
FourAlarmFire commented 6 months ago

I just get this error: Error in get_regulons(sce_SCENIC, column.attr.name = "Regulons") : The attribute 'Regulons' is not available in this loom file. The loom doesn't contain regulon information. when I tried to get the list of regulons of my pyscenic results regulons_incidMat<- get_regulons(sce_SCENIC, attrName="Regulons"), please someone could tell me where the issue is? thanks!!!

apal6 commented 1 week ago

Hi, I would like to follow up as I am having the same issue. Thank you so much!