Struct NormParams

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pub struct NormParams {
    pub logratio_trim: f64,
    pub sum_trim: f64,
    pub do_weighting: bool,
    pub a_cutoff: f64,
    pub quantile: f64,
}

Expand description

Tuning knobs for calc_norm_factors.

Names mirror edgeR’s: logratio_trim is logratioTrim, sum_trim is sumTrim, do_weighting is doWeighting, a_cutoff is Acutoff and quantile is p.

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§logratio_trim: f64

Fraction trimmed from each tail of the log-ratios. TMM and TMMwsp only.

§sum_trim: f64

Fraction trimmed from each tail of the abundances. TMM and TMMwsp only.

§do_weighting: bool

Weight each retained log-ratio by the inverse of its approximate asymptotic variance. TMM and TMMwsp only.

§a_cutoff: f64

Abundance floor; genes with a mean log-abundance at or below this are dropped before trimming. TMM only; edgeR’s TMMwsp ignores it.

§quantile: f64

Probability of the column quantile. NormMethod::UpperQuartile only.

Implementations§

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impl NormParams

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pub fn new( logratio_trim: f64, sum_trim: f64, do_weighting: bool, a_cutoff: f64, quantile: f64, ) -> Self

Builds a parameter set.

No validation here; calc_norm_factors checks the domains.

§Params

logratio_trim - Tail fraction trimmed from the log-ratios, in [0, 1)
sum_trim - Tail fraction trimmed from the abundances, in [0, 1)
do_weighting - Whether to use inverse-variance weights
a_cutoff - Abundance floor for TMM
quantile - Column quantile probability, in [0, 1]

§Returns

The parameter set.

Trait Implementations§

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impl Clone for NormParams

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fn clone(&self) -> Self

Returns a duplicate of the value. Read more

1.0.0 (const: unstable) · Source§

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source. Read more

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impl Copy for NormParams

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impl Debug for NormParams

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fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter. Read more

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impl Default for NormParams

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fn default() -> Self

edgeR’s defaults.

Auto Trait Implementations§

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impl UnwindSafe for NormParams

Blanket Implementations§

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impl<T> Any for T
where T: 'static + ?Sized,

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fn type_id(&self) -> TypeId

Gets the TypeId of self. Read more

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impl<T> Borrow<T> for T
where T: ?Sized,

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fn borrow(&self) -> &T

Immutably borrows from an owned value. Read more

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impl<T> BorrowMut<T> for T
where T: ?Sized,

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fn borrow_mut(&mut self) -> &mut T

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impl<T> ByRef<T> for T

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fn by_ref(&self) -> &T

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impl<ST, DT> CastableFrom<ST, Initialized, Initialized> for DT
where ST: ?Sized, DT: ?Sized,

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impl<ST, DT> CastableFrom<ST, Uninit, Uninit> for DT
where ST: ?Sized, DT: ?Sized,

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impl<T> CloneToUninit for T
where T: Clone,

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unsafe fn clone_to_uninit(&self, dest: *mut u8)

🔬This is a nightly-only experimental API. (clone_to_uninit)

Performs copy-assignment from self to dest. Read more

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impl<T> DistributionExt for T
where T: ?Sized,

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fn rand<T>(&self, rng: &mut (impl Rng + ?Sized)) -> T
where Self: Distribution<T>,

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impl<T> From<T> for T

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fn from(t: T) -> T

Returns the argument unchanged.

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impl<T, U> Imply<T> for U
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fn into(self) -> U

Calls U::from(self).

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fn into_either(self, into_left: bool) -> Either<Self, Self> ⓘ

Converts self into a Left variant of Either<Self, Self> if into_left is true. Converts self into a Right variant of Either<Self, Self> otherwise. Read more

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where F: FnOnce(&Self) -> bool,

Converts self into a Left variant of Either<Self, Self> if into_left(&self) returns true. Converts self into a Right variant of Either<Self, Self> otherwise. Read more

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