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hovestadtlab / conumee2

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To add more detail regions #4

Closed kwanghoon821 closed 6 days ago

kwanghoon821 commented 4 months ago

Hello.

I have a question about the detail region. If I want to add more genes to exclude or add, should I make the BED file like below? And read as a dataframe or something?

image

And what is the meaning of columns? 'score', 'probes_gene', 'probes_promoter'

Thank you!

bjarnedae commented 6 days ago

Hi,

thank you for your patience! You could use a customized BED file, but I recommend to modify the detail_regions GRanges object. You obtain it with:

data("detail_regions") (hg19) or data("detail_regions.hg38") (hg38)

The mentioned columns are optional and do not influence the analysis. Probes_gene shows how many probes are overlapping with the gene of interest, probes_promoter highlights the overlap with the gene promoter and score is deprecated and was removed in the latest release.

Kind regards, Bjarne