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About calling compartment PC1 values #327

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GleeenSIBS opened this issue May 8, 2023 · 1 comment
Open

About calling compartment PC1 values #327

GleeenSIBS opened this issue May 8, 2023 · 1 comment

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@GleeenSIBS
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Can GENOVA call compartment PC1 values by gene density or GC content? If I don‘t have an activate histone marker (peak file), how can I get PC1 values by GENOVA? Thanks!
@teunbrand
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Yes this is documented in ?sign_compartmentscore. For GC content, you can use a bedgraph and for gene density you can use a bed file of TSSs.

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@teunbrand @GleeenSIBS