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

In nolanlab/spade: SPADE -- An analysis and visualization tool for Flow Cytometry

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.

Note

Underlying implementations have been parallelized with OpenMP. Set OMP_NUM_THREADS in environment to control the number of threads used.

Author(s)

Michael Linderman

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"))

nolanlab/spade documentation built on May 23, 2019, 9:32 p.m.