Protein.normalize_reads

Protein.normalize_reads(method='CLR', jitter=0.5, scale=None, show_plot=False, random_state=None)

Normalize read counts.

This adds normalized_counts to the assay layers.

Parameters

methodstr

CLR, asinh, or NSP which stand for Centered Log Ratio, Inverse Hyperbolic transformation and Noise corrected and Scaled Protein counts respectively

jitterfloat

The standard deviation of the jitter to be added to the read counts before applying the normalization. The jitter is sampled from a normal distribution cenetered at 0. This is only applicable for NSP and asinh

scalefloat

The amount by which the read counts are scaled down. This is applicable only for NSP. If ‘None’ then the algorithm tries to estimate it from the read distribution.

show_plotbool

Whether to show diagnostic plots for NSP or not.

random_state: int

The random state to use for the NSP and asinh methods.

Raises

Exception

When one of the supported methods is not provided.