read.plateSet: Read FCS files from set of plates

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

Description

Reads all folders within the specified path containing the specified pattern in the folder names. Each folder contains a set a plate of FCS files. These folders typically make up a whole experiment. Plates are numbered according to the standard lexicographical ordering of your operating system.

Usage

read.plateSet(path = getwd(), pattern = "", ...)

Arguments

path	The path to search for folders containing FCS files
pattern	The regex pattern used to identify the folders of FCS files to be read
...	Additional arguments passed to read.flowSet. Note that 'alter.names' is forced to be TRUE in this implementation.

Value

A single flowSet containing all FCS files within the identified folders. The index of each folder in the list according to lexicographical ordering (1,2,...) is prepended to the sampleNames.

Examples

# Read in both of the example data sets as a single flowSet
plate1<-read.plateSet(path = system.file("extdata", package = "flowTime"),
pattern = "")

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