Could not find function "CreateChromatinAssay"

I am currently running an snATAC-seq analysis and performed the following command:

chrom_assay <- CreateChromatinAssay(
   counts = counts,
   sep = c(":", ","),
   genome = 'mm10', 
   fragments = ".../fragments.tbi", 
   min.cells = 10,
   min.features = 200
)

The error that comes out is: Error in CreateChromatinAssay. Could not find function "CreateChromatinAssay"

Any ideas on what to do? I've re-installed Signac multiple times and re-started the system. No progress.

atac-seq 10x cellranger snatac-seq

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updated 4.2 years ago by cpad0112

• written 4.2 years ago by bioinformatics.girl •

can you do this?

> grep ("CreateChromatinAssay", ls("package:Signac"), value = T)

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written 4.2 years ago by cpad0112

no item called "package::Signac" on the search list

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written 4.2 years ago by bioinformatics.girl •

Try this:

> library(Signac)
> ls("package:Signac")
> grep ("CreateChromatinAssay", ls("package:Signac"), value = T)

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written 4.2 years ago by cpad0112

It could be a disagreement between the package version and the exact command line.

https://github.com/timoast/signac/issues/195

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written 4.2 years ago by Mensur Dlakic

0 answers

No answers yet.

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