ReadInput {FlowSOM} | R Documentation |
Take some input and return FlowSOM object containing a matrix with the preprocessed data (compensated, transformed, scaled)
ReadInput( input, pattern = ".fcs", compensate = FALSE, spillover = NULL, transform = FALSE, toTransform = NULL, transformFunction = flowCore::logicleTransform(), transformList = NULL, scale = FALSE, scaled.center = TRUE, scaled.scale = TRUE, silent = FALSE )
input |
a flowFrame, a flowSet or an array of paths to files or directories |
pattern |
if input is an array of file- or directorynames, select only files containing pattern |
compensate |
logical, does the data need to be compensated |
spillover |
spillover matrix to compensate with
If |
transform |
logical, does the data need to be transformed |
toTransform |
column names or indices that need to be transformed.
Will be ignored if |
transformFunction |
Defaults to logicleTransform() |
transformList |
transformList to apply on the samples. |
scale |
logical, does the data needs to be rescaled |
scaled.center |
see |
scaled.scale |
see |
silent |
if |
FlowSOM object containing the data, which can be used as input for the BuildSOM function
# Read from file fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM") flowSOM.res <- ReadInput(fileName, compensate = TRUE, transform = TRUE, scale = TRUE) # Or read from flowFrame object ff <- flowCore::read.FCS(fileName) ff <- flowCore::compensate(ff, flowCore::keyword(ff)[["SPILL"]]) ff <- flowCore::transform(ff, flowCore::transformList(colnames(flowCore::keyword(ff)[["SPILL"]]), flowCore::logicleTransform())) flowSOM.res <- ReadInput(ff, scale = TRUE) # Build the self-organizing map and the minimal spanning tree flowSOM.res <- BuildSOM(flowSOM.res, colsToUse = c(9, 12, 14:18)) flowSOM.res <- BuildMST(flowSOM.res) # Apply metaclustering metacl <- MetaClustering(flowSOM.res$map$codes, "metaClustering_consensus", max = 10) # Get metaclustering per cell flowSOM.clustering <- metacl[flowSOM.res$map$mapping[, 1]]