motif analysis based on clusters

[kinali]

Hi all,

I got differentially accessible peaks for each cluster using FindAllMarkers() then I run the FindMotifs() for these peaks.
But, FindMotifs doesn't give cluster-based information. How can I obtain enriched motifs for each cluster?

note: I would like to find motifs for all of the clusters.

I appreciate any help,

[timoast]

If you provide a set of peaks specific to a certain cluster, then the motif enrichment results will be for that cluster

[kinali]

I guess as in this example when we specify clusters in FindMarkers we got that.

da_peaks <- FindMarkers(
object = mouse_brain,
ident.1 = 'Pvalb',
ident.2 = 'Sst',
only.pos = TRUE,
test.use = 'LR',
latent.vars = 'nCount_peaks'
)

enriched.motifs <- FindMotifs(
object = mouse_brain,
features = head(rownames(da_peaks), 1000)
)

But I would like to find enriched motifs for all the clusters, is that possible using Signac?

[timoast]

To find enriched motifs for all clusters, you need to find differential peaks for each cluster and run FindMotifs on the set of peaks for each cluster

[kinali]

I did that, but the result of the FindMotifs does not give cluster information. To do that, should I set the Motif data as in here
https://satijalab.org/signac/articles/data_structures.html then merge with the result of the FindMotifs?

[timoast]

I don't understand what you mean by it doesn't give cluster information...if you input a set of peaks that are specific to a cluster, then the enriched motifs returned are enriched in that cluster.

[kinali]

okay I understand, thank you^^