spade (version 1.20.0)

SPADE.addClusterToFCS: Annotate observations in FCS file with cluster assignment

Description

Annotate observations in a FCS file with cluster assignment

Usage

SPADE.addClusterToFCS(infilename, outfilename, clusterfilename, cols = NULL, arcsinh_cofactor=NULL, transforms=flowCore::arcsinhTransform(a=0, b=0.2), comp=TRUE)

Arguments

infilename

Name of input FCS file

outfilename

Name of output FCS file

clusterfilename

Name of FCS file with subset of cells used in clustering

cols

Usually a vector of strings specifying the columns to be used in the density calculation, e.g., c("(Cd110)D","(Cs111)D"). Strings will be matched against the parameter names extracted from the FCS file. The default=NULL will use all parameters.

arcsinh_cofactor

DEPRECATED. Cofactor used in arcsinh transform asinh(data/arcsinh_cofactor) of data.

transforms

Transform object to apply to data. A single transform object will be applied to all channels. To apply different transforms to specific channels use a named vector of transform objects (where names are parameter names).

comp

Apply compensation matrix if present in SPILL or SPILLOVER keywords

Value

The name of the written file is returned.

See Also

SPADE.FCSToTree

Examples

	# Not run
	## Load two-parameters sample data included in package
	#data_file_path = paste(installed.packages()["spade","LibPath"],"spade","extdata","SimulatedRawData.fcs",sep=.Platform$file.sep)

	#output_dir <- tempdir()
	#
	## Compute and annotate FCS file with density
	#density_file_path <- paste(output_dir,.Platform$file.sep,basename(data_file_path),".density.fcs",sep="")
	#SPADE.addDensityToFCS(data_file_path, density_file_path, cols=c("marker1","marker2"))

	## Downsample FCS file based on density
	#downsample_file_path <- paste(output_dir,.Platform$file.sep,basename(data_file_path),".density.fcs",sep="")
	#SPADE.downsampleFCS(density_file_path, downsample_file_path)

	## Create tree from downsampled FCS file
	#cells_file_path <- paste(output_dir,"clusters.fcs",sep="")
	#clust_file_path <- paste(output_dir,"clusters.table",sep="")
	#graph_file_path <- paste(output_dir,"mst.gml",sep="")
	#SPADE.FCSToTree(downsample_file_path, cells_file_path, graph_file_path, clust_file_path, cols=c("marker1","marker2"))

	## Add cluster to FCS files (known as "upsampling")
	#upsample_file_path <- paste(density_file_path,"cluster.fcs",sep=".")
	#SPADE.addClusterToFCS(density_file_path, upsample_file_path, cells_file_path, cols = c("marker1","marker2"))