GetMetaclusterCVs: GetMetaclusterCVs

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

GetMetaclusterCVs

Description

Compute the coefficient of variation for the metaclusters

Usage

GetMetaclusterCVs(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 CVs

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)
cvs <- GetMetaclusterCVs(flowSOM.res)

saeyslab/FlowSOM documentation built on July 6, 2024, 10:59 a.m.