readCytosploreFCS: Read .fcs files created by cytosplore

In KoenAStam/cytofast: cytofast - A quick visualization and analysis tool for CyTOF data

Read .fcs files created by cytosplore

Description

This function reads and combines .FCS files created specifcally by Cytosplore.

Usage

readCytosploreFCS(dir = NULL, colNames = c("names", "description"))

Arguments

dir	directory containing the .FCS files created by Cytosplore
colNames	character string that specifies which label should be used as the column names. This could be the name of the markers 'names' or the description for the markers 'description'.

Value

The function returns an object of class cfList.

Note

To succesfully read the .FCS files created by cytosplore make sure that there are no double channels. It could happen for example that the Cytosplore tag (CSPLR_ST) is added twice, which will most likely cause an error. Therefore, never add the sample tag twice. It is possible to remove the double tag in software like Flowjo.

As for the colNames parameter, both 'names' and 'description' will always work, it is up to the user to decide which one is most preferable.

This function is a wrapper around read.FCS. For more flexibility see their help page.

Examples

dirFCS <- system.file("extdata", package="cytofast")
cfData <- readCytosploreFCS(dir = dirFCS, colNames = "description")

KoenAStam/cytofast documentation built on June 1, 2022, 1:15 a.m.