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mt fraction calculation #39

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giovp opened this issue May 12, 2020 · 2 comments
Closed

mt fraction calculation #39

giovp opened this issue May 12, 2020 · 2 comments

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@giovp
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giovp commented May 12, 2020

In case you are planned to update tutorial at some point, Isaac pointed me to a cleaner way to calculate mt fraction.

adata.var["mt"] = adata.var_names.str.startswith("MT-")
sc.pp.calculate_qc_metrics(adata, qc_vars=["mt"], inplace=True)

It calculates both total_counts_mt and pct_counts_mt

just leaving it here as reference.
@LuckyMD
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LuckyMD commented May 12, 2020

yes, this function was added after the tutorial was finished ;). Thanks, though! Will leave this issue open for the grand update!

@le-ander le-ander mentioned this issue Dec 9, 2020
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@LuckyMD LuckyMD mentioned this issue Jan 5, 2021
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@LuckyMD
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LuckyMD commented Jan 5, 2021

Updated in #58

@LuckyMD LuckyMD closed this as completed Jan 5, 2021
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@LuckyMD @giovp