GetFeatures: GetFeatures

View source: R/2_buildSOM.R

GetFeaturesR Documentation

GetFeatures

Description

Map FCS files on an existing FlowSOM object

Usage

GetFeatures(
  fsom,
  files,
  level = c("clusters", "metaclusters"),
  type = "counts",
  MFI = NULL,
  positive_cutoffs = NULL,
  filenames = NULL,
  silent = FALSE
)

Arguments

fsom

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

files

Either a vector of FCS files or paths to FCS files

level

Level(s) of interest. Default is c("clusters", "metaclusters"), but can also be only one of them. Can be abbreviated.

type

Type of features to extract. Default is "counts", can be a vector of "counts", "percentages", "MFIs" and/or "percentages_positive" or abbreviations.

MFI

Vector with channels / markers for which the MFI values must be returned when "MFIs" is in type

positive_cutoffs

Named vector with fluorescence-intensity values per channel / marker that are the upper bounds for a negative population when "percentages_positive" is in type

filenames

An optional vector with filenames that will be used as rownames in the count matrices. If NULL (default) either the paths will be used or a numerical vector.

silent

Logical. If TRUE, print progress messages. Default = FALSE.

Value

matrix with features per population - type combination

Examples

 # Build FlowSom result
 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[1:1000, ], 
                        scale = TRUE, 
                        colsToUse = c(9, 12, 14:18),
                        nClus = 10)
   
 # Map new data
 counts <- GetFeatures(fsom = flowSOM.res, 
                       level = "clusters",
                       files = c(ff[1001:2000, ], ff[2001:3000, ]))
 features <- GetFeatures(fsom = flowSOM.res, 
                         files = c(ff[1001:2000, ], ff[2001:3000, ]),
                         type = c("counts", "percentages", "MFIs"), 
                         MFI = "APC-A", 
                         filenames = c("ff_1001-2000", "ff_2001-3000"))

 # Get percentages of positive cells
 positive_cutoffs <- c('CD8' = 1.5,
                       'CD4' = 0.3,
                       'CD19' = 1.3,
                       'CD3' = -0.3)
 
 perc_pos <- GetFeatures(fsom = flowSOM.res, 
                         files = c(ff[1001:2000, ], ff[2001:3000, ]),
                         type = c("percentages_positive"), 
                         positive_cutoffs = positive_cutoffs,
                         filenames = c("ff_1001-2000", "ff_2001-3000"))
                         

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