TestOutliers {FlowSOM} | R Documentation |
For every cluster, the distance from the cells to the cluster centers is
used to label cells which deviate too far as outliers. The threshold is
chosen as the median distance + mad_allowed
times the median absolute
deviation of the distances.
TestOutliers( fsom, mad_allowed = 4, fsom_reference = NULL, plot = FALSE, img_file = "testOutliers.pdf" )
fsom |
FlowSOM object |
mad_allowed |
Number of median absolute deviations allowed. Default = 4. |
fsom_reference |
FlowSOM object to use as reference. If NULL (default), the original fsom object is used. |
plot |
Should a plot be generated showing the distribution of the distances. Default is FALSE. |
img_file |
If plot is TRUE, the output will be written to this file. Default is "testOutliers.pdf" |
A new FlowSOM object
FlowSOMSubset
if you want to get a subset of the
current data instead of a new dataset
# Build FlowSom result fileName <- system.file("extdata", "68983.fcs", package="FlowSOM") ff <- flowCore::read.FCS(fileName) flowSOM.res <- FlowSOM(ff, compensate = TRUE, transform = TRUE, scale = TRUE, colsToUse = c(9, 12, 14:18), maxMeta = 10) # Map new data outlier_report <- TestOutliers(flowSOM.res)