Description Usage Arguments Details Value See Also Examples
modified readinput function from flowSOM for cases where data is not in fcs format but a data.table/frame
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input |
a flowFrame, a flowSet or an array of paths to files or directories or a data table or data frame |
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.
If |
transformFunction |
Defaults to logicleTransform() |
scale |
logical, does the data needs to be rescaled |
scaled.center |
see |
scaled.scale |
see |
silent |
if |
Take some input and return flowSOM object containing a matrix with the preprocessed data (compensated, transformed, scaled)
flowSOM object containing the data, which can be used as input for the BuildSOM function
1 2 3 4 5 6 7 8 9 10 11 12 | # Read from file
fileName <- system.file("extdata", "68983.fcs", package="flowSOM")
flowSOM.res <- ReadInputfrkn(fileName, compensate=TRUE,transform=TRUE,
scale=TRUE)
# Or read from flowFrame object
ff <- flowCore::read.FCS(fileName)
ff <- flowCore::compensate(ff,ff@description$SPILL)
ff <- flowCore::transform(ff,
flowCore::transformList(colnames(ff@description$SPILL),
flowCore::logicleTransform()))
flowSOM.res <- ReadInput(ff,scale=TRUE)
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