refine.spillover: Refine spillover coefficients

In carlosproca/autospill: AutoSpill: A method for calculating spillover coefficients to compensate or unmix high-parameter flow cytometry data

Description

Refines spillover coefficients iteratively.

Usage

refine.spillover(
  marker.spillover.unco.untr,
  marker.spillover.unco.tran,
  flow.gate,
  flow.control,
  asp
)

Arguments

marker.spillover.unco.untr	List of two matrices, with regressions intercepts and coefficients, resulting from the initial spillover calculation in untransformed scale.
marker.spillover.unco.tran	List of two matrices, with regressions intercepts and coefficients, resulting from the initial spillover calculation in transformed scale. Optional parameter used only in scatter plots, it can be NULL.
flow.gate	List of vectors with ids of gated events per sample.
flow.control	List with data and metadata of a set of controls.
asp	List with AutoSpill parameters.

Value

List with four elements:

• Spillover matrix at final step.

• Compensation matrix at final step.

• Compensation error at final step, a list with four matrices: intercepts, coefficients, slopes, and skewness.

• Dataframe with convergence data.

References

Roca et al: AutoSpill: A method for calculating spillover coefficients to compensate or unmix high-parameter flow cytometry data. bioRxiv 2020.06.29.177196; doi:10.1101/2020.06.29.177196 (2020).

See Also

get.marker.spillover, gate.flow.data, read.flow.control, and get.autospill.param.

carlosproca/autospill documentation built on Dec. 19, 2021, 1:52 p.m.