kaizhang/SnapATAC2

How to calculate TSS(UP 1K,DOWN 1K) score for gene of every cell?

mengchengyao opened this issue · 3 comments

mengchengyao commented

Hi,
Thanks for your great tools with single analysis tool.
Now I want to calculate TSS(Promoter region: UP 1K,DOWN 1K) score for gene of every cell, how can I do?
snapatac2.pp.make_gene_matrix
snapatac2.tl.init_network_from_annotation
snapatac2.metrics.frip

which function to use?
could you give an example ?

Yours

kaizhang commented

Currently, the closest function you can use is pp.make_gene_matrix which calculates the score using the whole gene body region: https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.make_gene_matrix.html#snapatac2.pp.make_gene_matrix

But the feature you requested is relatively easy to implement.

kaizhang commented

In v2.6.4, you will be able to achieve this by:

>>> gene_mat = snap.pp.make_gene_matrix(data, gene_anno=snap.genome.hg38, upstream=1000, downstream=1000, include_gene_body=False)
mengchengyao commented

In v2.6.4, you will be able to achieve this by:

>>> gene_mat = snap.pp.make_gene_matrix(data, gene_anno=snap.genome.hg38, upstream=1000, downstream=1000, include_gene_body=False)

Many thanks.