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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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rror in LinkPeaks #1698

Closed shabs24 closed 1 month ago

shabs24 commented 1 month ago

Hi,

I am trying to generate coverage plots for some of the genes that are expressed in my data. It works for other genes but not for these 3 genes and gives me an error

Testing 3 genes and 75234 peaks Error in LinkPeaks(object = WT, peak.assay = "ATAC", expression.assay = "SCT", : Could not find gene coordinates for requested genes

I can see the peaks in the promoter region in one of the genes and in the distal region in other gene in the annotation files.

Is it possible to plot the coverage around a gene even if it is not defined as peak.

This is the code I am using WT <- LinkPeaks( object = WT, peak.assay = "ATAC", expression.assay = "SCT", genes.use = genes )

Any suggestions?

timoast commented 1 month ago

The error message suggests that the genes you are requesting are not present in the gene annotations stored in the object.

Is it possible to plot the coverage around a gene even if it is not defined as peak.

Yes, a coverage plot can be created for any region of the genome

shabs24 commented 4 weeks ago

The error message suggests that the genes you are requesting are not present in the gene annotations stored in the object.

Is it possible to plot the coverage around a gene even if it is not defined as peak.

Yes, a coverage plot can be created for any region of the genome

Thanks for your help! I was able to resolve by adding lncRNA in my annotations while importing the genomic ranges from EnsDb.