SPADE.markerMedians: Compute marker medians, coefficient of variations and counts...

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

Description

Compute the marker medians, coefficients of variation and observations counts for cluster annoated FCS files.

Usage

SPADE.markerMedians(files, num.clusters, cols = NULL, arcsinh_cofactor=NULL, transforms=flowCore::arcsinhTransform(a=0, b=0.2), cluster_cols=NULL, comp=TRUE)
SPADE.annotateMarkers(files, cols = NULL, arcsinh_cofactor = 5)

Arguments

files	Name of input FCS file or vector of input FCS file names. FCS files must have "cluster" column.
num.clusters	Number of clusters. Note not all clusters need to be present in all files.
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).
cluster_cols	A vector of strings specifying columns that should be marked as having been used in clustering
comp	Apply compensation matrix if present in SPILL or SPILLOVER keywords

Details

SPADE.annotateMarkers is deprecated.

Value

List with:

count	Matrix of observation count for clusters
percenttotal	Matrix of percent of total number of cells [0-100] in each cluster
medians	Matrix of medians for specified columns
cvs	Matrix of coefficient of variation (CV), 100*sd(data)/abs(mean(data)), for specified columns

Author(s)

Michael Linderman

See Also

SPADE.addClusterToFCS, SPADE.annotateGraph

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)

	## Run basic SPADE analyses, clustering on two parameters. 
	#output_dir <- tempdir()
	#SPADE.driver(data_file_path, out_dir=output_dir, cluster_cols=c("marker1","marker2"))

	## Compute medians, counts and other parameters from processed files
	#upsampled_file_path <- paste(output_dir,.Platform$file.sep,basename(data_file_path),".density.fcs.cluster.fcs",sep="")
	#mst_graph <- igraph:::read.graph(paste(output_dir,"mst.gml",sep=.Platform$file.sep),format="gml")
	#anno <- SPADE.markerMedians(upsampled_file_path, igraph:::vcount(mst_graph), cols = c("marker1","marker2"))

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