Description Usage Arguments Value Author(s) Examples
Helper function for flattening list of annotations
1 | SPADE.flattenAnnotations(annotations)
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annotations |
A list of annotation matrices. All matrices must have the same number of rows. |
Single matrix of annotations
Michael Linderman
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | # 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"))
## Flatten annotations so they can easily be saved in table
#flat_anno <- SPADE.flattenAnnotations(anno)
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