GetMetaclusterPercentagesPositive: Get percentage-positive values for all metaclusters

View source: R/4_metaClustering.R

GetMetaclusterPercentagesPositiveR Documentation

Get percentage-positive values for all metaclusters

Description

Get percentage-positive values for all metaclusters

Usage

GetMetaclusterPercentagesPositive(
  fsom,
  cutoffs,
  colsUsed = FALSE,
  prettyColnames = FALSE
)

Arguments

fsom

FlowSOM object as generated by the FlowSOM function or the BuildSOM function

cutoffs

named numeric vector. Upper bounds of negative population fluorescence-intensity values for each marker / channel.

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

Matrix with percentages of cells that are positive in selected markers per each metacluster

Examples

fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM")
flowSOM.res <- FlowSOM(fileName, compensate = TRUE, transform = TRUE,
                      scale = TRUE, colsToUse = c(9, 12, 14:18), nClus = 10)
perc_pos <- GetMetaclusterPercentagesPositive(flowSOM.res, cutoffs = c('CD4' = 5000))

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