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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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Only show Links associated with promoter #1710

Closed KunFang93 closed 6 months ago

KunFang93 commented 6 months ago

Hi,

I wondered if we could modify the contains of Links(RTCS.cancer.atac.seu) to show only links that related to promoter? I generated links with following codes

RTCS.cancer.atac.conns <- run_cicero(RTCS.cancer.atac.cicero, genomic_coords = genome.df, sample_num = 150)
RTCS.cancer.atac.ccans <- generate_ccans(RTCS.cancer.atac.conns)
RTCS.cancer.atac.links <- ConnectionsToLinks(conns = RTCS.cancer.atac.conns, ccans = RTCS.cancer.atac.ccans)
Links(RTCS.cancer.atac.seu) <- RTCS.cancer.atac.links

I try to filter some rows but I am not sure how to interpret group column.. I wondered if you could shed some light on it? If possible, I also wondered how we retrieve regions(peak) of those the Links associated with promoters in a list of genes? Thanks in advance!

Best, Kun

KunFang93 commented 6 months ago

I figured it out. start is a position in loc1 and end is a position in loc2 and nothing to do with group column.