set2DF: convert a flowSet to a data frame

In hzc363/CytoDx: Robust prediction of clinical outcomes using cytometry data without cell gating

Description

A function that convert a flowSet to a data frame.

Usage

set2DF(flowSet, fcsFiles, y = NULL)

Arguments

flowSet	A flowSet object
fcsFiles	A vector containing the name of each fcs file included in flowSet.
y	The clinical outcome each fcs file associated with. Null for testing data.

Value

Returns a data frame containing the cytometry data. Cells from different fcs files are combined into one flow frame. A new column, xSample, is introduced to indicate the origin of each cell. The data frame also includes the clinical outcome y.

Examples

library(flowCore)
# Find the table containing fcs file names in CytoDx package
path <- system.file("extdata",package="CytoDx")
# read the table
fcs_info <- read.csv(file.path(path,"fcs_info.csv"))
# Specify the path to the cytometry files
fn <- file.path(path,fcs_info$fcsName)
fSet <- read.flowSet(fn)
df <- set2DF(flowSet=fSet,fcsFiles=fn,y = fcs_info$Label)

hzc363/CytoDx documentation built on May 8, 2019, 11:56 p.m.