Debarcode

Debarcodes FlowCode data, identifying valid and invalid combinations.

Usage

debarcode(unmixed, flowcode.fluors, flowcode.thresholds, combo.df)

Arguments

unmixed

Matrix of unmixed flow cytometry expression data. Cells in rows and fluorophores in columns. Fluorophores must include flowcode.fluors.

flowcode.fluors

Named character vector of fluorophores used to identify the FlowCodes. Names should be FlowCode epitope tags, values should be the corresponding fluorophores.

flowcode.thresholds

Named numeric vector of thresholds above which the cell (event) may be considered positive for a given FlowCode. Names should be fluorophores, values should be the threshold in raw, untransformed unmixed scale.

combo.df

Data frame describing the valid combinations of FlowCodes. Structure: One row per combination. Columns are Id, Procode.tag1, Procode.tag2 and Procode.tag3, describing the name (e.g., CRISPR target), and three epitopes for the combination, respectively.

Value

A numeric vector, length nrow(unmixed), linking each event to an Id in combo.df by row number.