meta.export {immunoClust} | R Documentation |
Thess functions collect the output of the meta.process
and
extracts the event numbers, relative frequencies or mean fluorescence
intensities for each meta-cluster and cell-clustering experiment in a numeric
table.
meta.numEvents(meta, out.all=TRUE, out.removed=FALSE, out.unclassified=TRUE) meta.relEvents(meta, out.all=TRUE) meta.parMFI(meta, par, out.all=TRUE) meta.numClusters(meta, out.all=TRUE) meta.freqTable(meta) meta.relEvents2(meta, major=1:5, out.all=TRUE) meta.relEvents3(meta, major=1:5, out.all=TRUE) meta.majorEvents(meta, major=1:6, out.events=TRUE)
meta |
The list-object returned by the function meta.process. |
par |
An integer index to the specific parameter. |
out.all |
A numeric indicator whether the event numbers of all hierarchical gating levels are obtained or only the meta-clusters themselves. |
out.removed |
A numeric indcator whether the number of removed events, which are not used for clustering are exported. |
out.unclassified |
A numeric indicator whether the event numbers of the hierarchical gating levels or all meta-clusters are exported. |
out.events |
Switch between cell event numbers and relative cell frequencies. |
major |
A numeric array indication the major scatter regions which were used as total events. |
A numberic matrix with
the number of cell events
relative frequencies, i.e. the number of cell events per total meeasured events
mean fluorecence intensities in one parameter, i.e. the meta-cluster centers in asinh-tranformed scale
the number of cell clusters
relative frequencies with respect to all gating hierarchie levels
prelimary function; as relEvents but is restricted to the events in the given major scatter regions.
prelimary function; union of relEvents and relEvents2
the number of cell events for the major regions only
in each meta-cluster (and gating hierarchy level) for each cell-clustering experiment.
Till Sörensen till-antoni.soerensen@charite.de
Sörensen, T., Baumgart, S., Durek, P., Grützkau, A. and Häupl, T. immunoClust - an automated analysis pipeline for the identification of immunophenotypic signatures in high-dimensional cytometric datasets. Cytometry A (submitted).
data(dat.exp) meta <- meta.process(dat.exp) tbl <- meta.numEvents(meta)