GetMarkers: GetMarkers

In SofieVG/FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

GetMarkers

Description

Get marker names for an array of channels, given a flowFrame or a FlowSOM object. As available in "desc". If this is NA, defaults to channel name. grep is used to look for the markers. Other regex can be added.

Usage

GetMarkers(object, channels, exact = TRUE)

Arguments

object	The flowFrame or the FlowSOM object of interest
channels	Vector with markers or channels of interest. Also accepts the index of the channel in the object.
exact	If TRUE (default), the grep pattern will be extended to start with ^\\Q and end with \\E$, so only exact matches are possible.

Value

Corresponding marker names

See Also

GetChannels

Examples

   # Read the flowFrame
   fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM")
   ff <- flowCore::read.FCS(fileName)
   GetChannels(ff, c("FSC-A", "CD3", "FITC-A"))
   GetMarkers(ff, c("FSC-A", "CD3", "FITC-A"))

SofieVG/FlowSOM documentation built on Feb. 1, 2024, 11:33 a.m.