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cellbin gem_reader.gem2anndata binszie参数设置 #3

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seqyuan opened this issue Nov 1, 2024 · 1 comment
Open

cellbin gem_reader.gem2anndata binszie参数设置 #3

seqyuan opened this issue Nov 1, 2024 · 1 comment

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@seqyuan
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seqyuan commented Nov 1, 2024

我使用的是cellbin的gem,采用Gem_Reader成功读入了数据 ,想转化成anndata,
示例是下面这样写的:
adata_bin200 = gem_reader.gem2anndata(200)
我查阅到binsize 默认设置的是50,请问cellbin应该怎样设置gem_reader.gem2anndata的binsize参数

@liuxingnancy
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首先构建Gem_Reader对象的时候指定cell label列名,比如列名为“label”:
gem_reader = Gem_Reader(gem_file, cell_label_key="label")
然后直接用function cellbin2anndata来转换:
adata = gem_reader.cellbin2anndata()

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