addbs: Add background subtraction to a summary data frame

In flowTime: Annotation and analysis of biological dynamical systems using flow cytometry

Description

Subtracts the background fluorescence of a given control strain from the chosen column.

Usage

addbs(
  flowData,
  column = "FL3.Amean",
  baseline_column = "strain",
  baseline = "noYFP"
)

Arguments

flowData	the summary data frame of flowSet to be background subtracted
column	the column containing the fluorescent measurement to be background subtracted
baseline_column	the column containing the name of the strain representing background fluorescent values
baseline	character the name of the strain representing background fluorescent values

Value

A summary data frame with an additional column "column_bs" containing the background subtracted fluorescent values

Examples

dat<-read.flowSet(path=system.file("extdata", "tc_example",
package = "flowTime"),alter.names = TRUE)
annotation <- read.csv(system.file("extdata", "tc_example.csv",
package = "flowTime"))
annotation[which(annotation$treatment == 0), 'strain'] <- 'background'
adat <- annotateFlowSet(dat, annotation)
loadGates(gatesFile = 'C6Gates')
dat_sum <- summarizeFlow(adat, ploidy = 'diploid', only = 'singlets',
channel = 'FL1.A')
dat_sum <- addbs(dat_sum, column = "FL1.Amean", baseline = "background")

flowTime documentation built on Nov. 8, 2020, 8:13 p.m.