GetMetaclusterMFIs: GetMetaclusterMFIs

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

GetMetaclusterMFIs

Description

Compute the median fluorescence intensities for the metaclusters

Usage

GetMetaclusterMFIs(fsom, colsUsed = FALSE, prettyColnames = FALSE)

Arguments

fsom	Result of calling the FlowSOM function
colsUsed	Logical. Should report only the columns used to build the SOM. Default = FALSE.
prettyColnames	Logical. Should report pretty column names instead of standard column names. Default = FALSE.

Value

Metacluster MFIs

Examples

fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM")
ff <- flowCore::read.FCS(fileName)
ff <- flowCore::compensate(ff, flowCore::keyword(ff)[["SPILL"]])
ff <- flowCore::transform(ff,
         flowCore::transformList(colnames(flowCore::keyword(ff)[["SPILL"]]),
                                flowCore::logicleTransform()))
flowSOM.res <- FlowSOM(ff,
                       scale = TRUE,
                       colsToUse = c(9, 12, 14:18),
                       nClus = 10)
mfis <- GetMetaclusterMFIs(flowSOM.res)

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