Suggestion: a function to send TSSes to seqArchR

[charles-plessy]

I think that it would be quite straightforward to send the dominant TSS from tag clusters or consensus clusters to @snikumbh 's seqArchR package; something along these lines:

bsgenome <- getBSgenome(unique(genome(clusters)))
inputSeqsRaw <- clusters$dominant_ctss |> promoters(100,100) |> trim() |> getSeq (x = bsgenome) |> suppressWarnings()
inputSeqsRaw <- inputSeqsRaw[width(inputSeqsRaw) == 200] # remove trimmed sequences
inputSeqsMat <- seqArchR::get_one_hot_encoded_seqs(seqs = inputSeqsRaw, sinuc_or_dinuc = "dinuc")
inputSeqsMat <- seqArchR::get_one_hot_encoded_seqs(seqs = inputSeqsRaw, sinuc_or_dinuc = "dinuc")
# Etc following seqArchR's doc.