addbs: Add background subtraction to a summary data frame

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

Add background subtraction to a summary data frame

Description

Makes a new column from column with the background value of a given baseline control from a chosen identifier column baseline_column subtracted from the values of column.

Usage

addbs(data, column, baseline_column, baseline = "noYFP")

Arguments

data	the summary data frame of a flowSet (from summarizeFlow or flsummary) to be used in calculating the background subtracted column
column	the column containing the fluorescent (or other) measurement to be background subtracted
baseline_column	the column containing the identifier of the rows containing background values
baseline	character the identified or name of representing background fluorescent values

Value

A summary data frame with an additional column column_bs containing the background subtracted 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)
dat_sum <- summarizeFlow(adat, gated = TRUE,
channel = 'FL1.A')
dat_sum <- addbs(data = dat_sum, column = FL1.Amean,
baseline_column = strain,
baseline = "background")

wrightrc/flowTime documentation built on Dec. 8, 2022, 9:50 p.m.