kipoi_veff.scores

Ref

Ref(self, rc_merging='mean')

Returns the predictions for the reference allele.

If the predictions were executed taking the reverse-complement of the sequence into account then the returned value is averaged by the function defined in rc_merging. Allowed values for rc_merging are: "min", "max", "mean", "median", "absmax" or any callable that accepts/expects two arguments: my_func(fwd_pred, rc_pred).

Reverse-complement-averaging, where applicable, is performed after score calculation.

Alt

Alt(self, rc_merging='mean')

Returns the predictions for the alternative allele.

If the predictions were executed taking the reverse-complement of the sequence into account then the returned value is averaged by the function defined in rc_merging. Allowed values for rc_merging are: "min", "max", "mean", "median", "absmax" or any callable that accepts/expects two arguments: my_func(fwd_pred, rc_pred).

Reverse-complement-averaging, where applicable, is performed after score calculation.

Diff

Diff(self, rc_merging='mean')

Returns the difference between predictions for the reference and alternative sequences prediction difference: diff = p_alt - p_ref

If the predictions were executed taking the reverse-complement of the sequence into account then the returned value is averaged by the function defined in rc_merging. Allowed values for rc_merging are: "min", "max", "mean", "median", "absmax" or any callable that accepts/expects two arguments: my_func(fwd_pred, rc_pred).

Reverse-complement-averaging, where applicable, is performed after score calculation.

LogitRef

LogitRef(self, rc_merging='mean')

Returns the predictions for the reference allele on the logit scale: np.log(p_alt / (1 - p_alt )).

If the predictions were executed taking the reverse-complement of the sequence into account then the returned value is averaged by the function defined in rc_merging. Allowed values for rc_merging are: "min", "max", "mean", "median", "absmax" or any callable that accepts/expects two arguments: my_func(fwd_pred, rc_pred).

Reverse-complement-averaging, where applicable, is performed after score calculation.

LogitAlt

LogitAlt(self, rc_merging='mean')

Returns the predictions for the alternative allele on the logit scale: np.log(p_alt / (1 - p_alt ))

If the predictions were executed taking the reverse-complement of the sequence into account then the returned value is averaged by the function defined in rc_merging. Allowed values for rc_merging are: "min", "max", "mean", "median", "absmax" or any callable that accepts/expects two arguments: my_func(fwd_pred, rc_pred).

Reverse-complement-averaging, where applicable, is performed after score calculation.

Logit

Logit(self, rc_merging='mean')

Returns the difference between predictions for the reference and alternative sequences on the logit scale: logit_diff = log(p_alt / (1 - p_alt )) - log(p_ref / (1 - p_ref ))

If the predictions were executed taking the reverse-complement of the sequence into account then the returned value is averaged by the function defined in rc_merging. Allowed values for rc_merging are: "min", "max", "mean", "median", "absmax" or any callable that accepts/expects two arguments: my_func(fwd_pred, rc_pred).

Reverse-complement-averaging, where applicable, is performed after score calculation.

DeepSEA_effect

DeepSEA_effect(self, rc_merging='mean')

Returns the score used by DeepSEA in order to calculate the e-value: abs(logit_diff) * abs(diff)

If the predictions were executed taking the reverse-complement of the sequence into account then the returned value is averaged by the function defined in rc_merging. Allowed values for rc_merging are: "min", "max", "mean", "median", "absmax" or any callable that accepts/expects two arguments: my_func(fwd_pred, rc_pred).

Reverse-complement-averaging, where applicable, is performed after score calculation.