effect

Below is an auto-generated summary of the xftsim.effect submodule API.

Summary

class xftsim.effect.AdditiveEffects(beta, variant_indexer=None, component_indexer=None, standardized=True, scaled=True)

Bases: object

Additive genetic effects object. Given matrix / vector of effects will provide various scalings / offsets for computation

Parameters:

  • beta (NDArray[Any, Any]) – Vector of diploid effects

  • variant_indexer (xft.index.HaploidVariantIndex | xft.index.DiploidVariantIndex) – Variant indexer, will determine ploidy automatically

  • component_indexer (xft.index.ComponentIndex, optional) – Phenotype component indexer, defaults to xft.index.ComponentIndex.RangeIndex if not provided

  • standardized (bool, optional) – True implies these are effects of standardized variants, by default True

  • scaled (bool, optional) – True implies these are effects of variants * sqrt(m_causal), by default True

AF

diploid allele frequencies

Type:

NDArray

beta_scaled_standardized_diploid

Diploid effects scaled of standardized variants multiplied by number of causal variants per phenotype

Type:

NDArray

beta_scaled_standardized_haploid

haploid variant of above

Type:

NDArray

beta_scaled_unstandardized_diploid

Diploid effects scaled of unstandardized variants multiplied by number of causal variants per phenotype

Type:

NDArray

beta_scaled_unstandardized_haploid

haploid variant of above

Type:

NDArray

beta_unscaled_standardized_diploid

Diploid effects scaled of standardized variants unscaled by number of causal variants per phenotype

Type:

NDArray

beta_unscaled_standardized_haploid

haploid variant of above

Type:

NDArray

beta_unscaled_unstandardized_diploid

Diploid effects scaled of unstandardized variants unscaled by number of causal variants Multiply these against (0,1,2) raw genotypes and subtract offset to obtain phenotypes

Type:

NDArray

beta_unscaled_unstandardized_haploid

Haploid variant of above

Type:

NDArray

beta_raw_diploid

Alias for beta_unscaled_unstandardized_diploid

Type:

NDArray

beta_raw_haploid

Alias for beta_unscaled_unstandardized_haploid

Type:

NDArray

component_indexer
Type:

xft.index.ComponentIndex

k

Number of phenotypes (columns of effect matrix)

Type:

int

m

Number of diploid variants

Type:

int

offset

To compute phenotypes, add offset after multiplying by beta_raw_* to mean deviate under HWE

Type:

NDArray

variant_indexer
Type:

xft.index.HaploidVariantIndex

property beta_raw_diploid
property beta_raw_haploid
property beta_scaled_standardized_haploid
property beta_scaled_unstandardized_haploid
property beta_unscaled_standardized_haploid
property beta_unscaled_unstandardized_haploid
corr()
property m_causal
property offset
class xftsim.effect.GCTAEffects(vg, variant_indexer=None, component_indexer=None)

Bases: AdditiveEffects

Additive genetic effects object under GCTA infinitessimal model <CITE>

Under this genetic architecture, all variants are causal and standardized genetic variants / sqrt(m) have the user specified (possibly diagonal) variance covariance matrix

Parameters:

  • vg (Iterable | NDArray) – Vector of genetic variances or genetic variance/covariance matrix

  • variant_indexer (xft.index.HaploidVariantIndex | xft.index.DiploidVariantIndex) – Variant indexer, will determine ploidy automatically

  • component_indexer (xft.index.ComponentIndex, optional) – Phenotype component indexer, defaults to xft.index.ComponentIndex.RangeIndex if not provided

class xftsim.effect.NonOverlappingEffects(vg, proportions=None, variant_indexer=None, component_indexer=None, permute=True)

Bases: AdditiveEffects

Additive genetic effects object under non-infinitessimal model with no pleoitropy

Under this genetic architecture, the genome is partitioned into k+1 components corresponding to k sets of variants corresponding to those causal for each trait together with a final set of variants not causal for any traits. Within each kth set of causal variants, standardized variants are Gaussian with variance vg[k] / sqrt(proportions[k])

Parameters:

  • vg (Iterable) – Vector of genetic variances or genetic variance/covariance matrix

  • proportions (Iterable) – Proportion of variants causal for each trait. If an extra value is provided, this will be the number of variants that are noncausal for all traits. Defaults to an equal number of variants per trait

  • permute (bool) – Permute variants? If False, causal variants for each phenotype will fall into contiguous blocks, defaults to True

  • variant_indexer (xft.index.HaploidVariantIndex | xft.index.DiploidVariantIndex) – Variant indexer, will determine ploidy automatically

  • component_indexer (xft.index.ComponentIndex, optional) – Phenotype component indexer, defaults to xft.index.ComponentIndex.RangeIndex if not provided