ProcessGatingML: Process a gatingML file

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

Description

Reads a gatingML file using the flowUtils library and returns a list with a matrix containing filtering results for each specified gate and a vector with a label for each cell

Usage

ProcessGatingML(flowFrame, gatingFile, gateIDs, cellTypes, silent = FALSE)

Arguments

flowFrame	The flowFrame to apply the gating on
gatingFile	The gatingML file to read
gateIDs	Named vector containing ids to extract from the gatingML file to use in the matrix
cellTypes	Cell types to use for labeling the cells. Should be a subset of the names of the gateIDs
silent	If FALSE, show messages of which gates are being processed

Value

This function returns a list in which the first element ("matrix") is a matrix containing filtering results for each specified gate and the second element ("manual") is a vector which assigns a label to each cell

See Also

PlotPies

Examples

   # Read the flowFrame
   fileName <- system.file("extdata","lymphocytes.fcs",package="FlowSOM")
   ff <- flowCore::read.FCS(fileName)
   ff_c <- flowCore::compensate(ff,flowCore::description(ff)$SPILL)
   flowCore::colnames(ff_c)[8:18] <- paste("Comp-",
                                     flowCore::colnames(ff_c)[8:18],
                                     sep="")

   # Specify the gating file and the gates of interest
   gatingFile <- system.file("extdata","manualGating.xml",
                             package="FlowSOM")
   gateIDs <- c( "B cells"=8,
                 "ab T cells"=10,
                 "yd T cells"=15,
                 "NK cells"=5,
                 "NKT cells"=6)
   cellTypes <- c("B cells","ab T cells","yd T cells",
                 "NK cells","NKT cells")
   gatingResult <- ProcessGatingML(ff_c, gatingFile, gateIDs, cellTypes)


   # Build a FlowSOM tree
   flowSOM.res <- FlowSOM(ff_c,compensate=FALSE,transform=TRUE,
                         toTransform=8:18,colsToUse=c(9,12,14:18),nClus=10)
   # Plot pies indicating the percentage of cell types present in the nodes
   PlotPies(flowSOM.res[[1]],gatingResult$manual)

FlowSOM documentation built on Nov. 17, 2017, 10:04 a.m.