summarizeFlow: Generate summary statistics for a flowSet

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

Generate summary statistics for a flowSet

Description

Gates a sample to all yeast, then singlet, then doublets. Also calculates singlet to doublet ratio. Returns a list of data frames, e.g. output$singlets, output$doublets, etc.

Usage

summarizeFlow(
  flowset,
  channel = NA,
  gated = FALSE,
  ploidy = FALSE,
  only = FALSE
)

Arguments

flowset	the flowSet to be summarized
channel	character vector which data channel(s) should be summarized? If excluded (or NA) all channels will be summarized (default)
gated	boolean is the data already appropriately gated?
ploidy	character does the flowSet contain haploid or diploid cells?
only	character summarize only "singlet", "doublet", or all "yeast" cells, FALSE will return all

Value

data frame containing the specified summary statistics of the specified cell populations for each frame

Examples

plate1 <- read.flowSet(path = system.file("extdata", "ss_example",
package = "flowTime"), alter.names = TRUE)
summarizeFlow(plate1, channel = "FL1.A", gated = TRUE,
ploidy = "diploid", only = "yeast")

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