GetFeatures: GetFeatures

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

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"))
                         

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