Create ATAC-pseudobulk from a list of cells for peak-gene links #1754
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Hi all, I have worked myself through the manual and now have my PeakToGeneLinks. I have now generated knn-based lists of cell labels to make pseudo-bulks. My first question now is: Is there a simple/inbuilt way to aggregate these cell lists to pseudo-bulk-peaks? Preferably I would want to use the peak regions found using "10.1 The Iterative Overlap Peak Merging Procedure". I know there is a categorization of peaks in Distal, Exonic, Intronic and Promoter, but I did not find a way how to get which peak belongs to which category (I would assume that is also gene specific) except a old homebrew solution (#838) My second question is: Is there a inbuilt way to get this information for each peak-gene-link nowadays? It doesn't show up as a column when I use getPeak2GeneLinks. Lastly, there is no category “gene body”, in the peaks list or at least I found none. My last question is how to create such pseudo-bulk-peaks (as described in question 1) for specific regions, for example the gene bodies of all genes. Can this be done in ArchR, or do I need to use MACS2 for that. Many thanks in advance! |
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Replies: 2 comments
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Add a new columne to cellColData defining whatever cell groupings you want and then provide that to
We dont provide functions for every operation one might want to perform. Some things like this just require a little manual code to perform. All of the info is there, as shown in the post you linked.
Gene body is not a relevant category beyond exonic and intronic.
No. You would create the peak set as described above and then subset that peak set to your regions of interest |
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Thank you for your answer! |
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Add a new columne to cellColData defining whatever cell groupings you want and then provide that to
addReproduciblePeakSet()groupbyparam.We dont provide functions for every operation one might want to perform. Some things like this just require a little manual code to perform. All of the info is there, as shown in the post you linked.