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buenrostrolab / FigR

Functional Inference of Gene Regulation
https://buenrostrolab.github.io/FigR/
MIT License
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Error in runGenePeakcorr #21

Open Genki-YAN opened 1 year ago

Genki-YAN commented 1 year ago

I have checked the format of the ATAC.se and the RNAmat.They are SummarizedExperiment and matrix. But when I ran runGenePeakcorr, I still have this problem.

cisCorr <- runGenePeakcorr(ATAC.se = ATAC.rs.paired,
                           RNAmat = as.matrix(RNAmat.paired@assays$RNA@counts),
                           genome = "mm10", # One of hg19, mm10 or hg38
                           nCores = 4,
                           p.cut = NULL, # Set this to NULL and we can filter later
                           n_bg = 100)

Assuming paired scATAC/scRNA-seq data .. Error in centerCounts(ATACmat) : Supplied object must be either of class SummarizedExperiment or Matrix ..

Can someone solve this? Thanks! image

image

vkartha commented 1 year ago

Hi @Genki-YAN , can you simply print your ATAC.rs.paired object (type the object name and hit enter and paste the contents here?) Can you also show me the contents of running assay(ATAC.rs.paired)[1:5,1:5]?

This seems to be a format check issue (either the object isn't what we're expecting or the check is throwing an error for an improper reason which I would fix)

Thanks

ajt986 commented 1 year ago

Hi, In case others may run into this issue: Make sure that the count matrix supplied to the SummarizedExperiment is of type Matrix from the Matrix library and not matrix. This fixed the issue for me at least.