| GetFeatures {FlowSOM} | R Documentation |
Map fcs files on an existing FlowSOM object
GetFeatures(
fsom,
files,
level = c("clusters", "metaclusters"),
type = "counts",
MFI = NULL,
filenames = NULL,
silent = FALSE
)
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 |
type |
Type of features to extract. Default is "counts", can be a vector of "counts", "percentages" and/or "MFIs" |
MFI |
Vector with channels / markers for which the MFI
values must be returned when "MFIs" is in |
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 |
matrix with features per population - type combination
# 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"))