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FEAT: Implement Likelihood-Ratio test #178

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FEAT: Implement Likelihood-Ratio test #178

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589d70e
initial commit
PABannier Oct 17, 2023
1a95da8
arg sanity check
PABannier Oct 17, 2023
86cf0e0
setup wald and LRT
PABannier Oct 17, 2023
4a663d0
implemented lrt test
PABannier Oct 17, 2023
570f881
fix and test on example
bbdnr Oct 17, 2023
4289521
minor errors
alexandrenowak Oct 17, 2023
e2afb7d
cosmit
PABannier Oct 17, 2023
b913d20
cosmit
PABannier Oct 17, 2023
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initial commit
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@PABannier
PABannier committed Oct 17, 2023
commit 589d70e440b1b2ada58f9d9f2d94996e4b00b340
2 changes: 2 additions & 0 deletions pydeseq2/ds.py
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Original file line number Diff line number Diff line change
Expand Up @@ -146,6 +146,7 @@ class DeseqStats:
def __init__(
self,
dds: DeseqDataSet,
test: Literal["Wald", "LRT"] = "Wald",
contrast: Optional[List[str]] = None,
alpha: float = 0.05,
cooks_filter: bool = True,
Expand All @@ -167,6 +168,7 @@ def __init__(
self.dds = dds

self.alpha = alpha
self.test = test
self.cooks_filter = cooks_filter
self.independent_filter = independent_filter
self.base_mean = self.dds.varm["_normed_means"].copy()
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