scallops.reads.channel_crosstalk_matrix

scallops.reads.channel_crosstalk_matrix(a, method='median', by_t=False, **kwargs)

Estimate and correct differences in channel intensity and spectral overlap among sequencing channels using either median or Li and Speed method.

Describe with linear transformation w so that w * a = y, where y is the corrected data.

Parameters:

• a (DataArray) – data to compute crosstalk matrix for (read, t, c)

• by_t (bool) – Compute separate matrices per cycle.

• method (Literal['median', 'li_and_speed']) – Either median or li_and_speed

Returns:

The inverse matrix, w (c,c) or an array of (t, c, c) if by_t

Return type:

ndarray | Array | dict[str, list[str] | ndarray]