Wrapper for LuciernagaQC for large scale profiling. Matches unstained with single colors for respective dates, extracts signature and plots, returns data.frame and list of patchwork objects.

Wrapper for LuciernagaQC for large scale profiling. Matches unstained with single colors for respective dates, extracts signature and plots, returns data.frame and list of patchwork objects.

Usage

Luciernaga_SignatureExternalUnstained(
  x,
  UnstainedList,
  FluorophoreList,
  Multiple = FALSE,
  GateTemplatePath,
  removestrings = ".fcs",
  AFOverlap,
  controlType,
  subsets
)

Arguments

x

The list of Dates

UnstainedList

The list of file.paths for the unstained files

FluorophoreList

The list of file.paths for the fluorophore files

Multiple

Default FALSE, if expecting multiple single color controls per unstained set TRUE

GateTemplatePath

File.path to the openCyto gating template .csv

removestrings

Default is ".fcs", removes from name

AFOverlap

File.path to LuciernagaQC AFOverlap .csv to handle exceptions.

controlType

Either "beads" or "cells" (selects respective external AF protocol)

subsets

The desired openCyto gating population to extract signature from

Value

A data.frame and a list of patchwork plots

Examples

library(Luciernaga)