meta.export: immunoClust Meta-clustering Results Export

In immunoClust: immunoClust - Automated Pipeline for Population Detection in Flow Cytometry

Description

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.

Usage

meta.numEvents(meta, out.all=TRUE, out.removed=FALSE,  out.unclassified=TRUE)
meta.relEvents(meta, out.all=TRUE)
meta.relParent(meta, out.all=TRUE, out.removed=FALSE,  out.unclassified=TRUE)

meta.parMFI(meta, par, out.all=TRUE)

meta.numClusters(meta, out.all=TRUE)

meta.freqTable(meta)

Arguments

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.

Value

A numberic matrix with

numEvents

the number of cell events

relEvents

relative frequencies, i.e. the number of cell events per total meeasured events

relParent

relative frequencies according to parent relationship in the annotated hierarchy.

parMFI

mean fluorecence intensities in one parameter, i.e. the meta-cluster centers in asinh-tranformed scale

numClusters

the number of cell clusters

freqTable

relative frequencies with respect to all gating hierarchie levels

in each meta-cluster (and gating hierarchy level) for each cell-clustering experiment.

Author(s)

Till Sörensen [e-mail]

References

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).

See Also

meta.process

Examples

data(dat.exp)
meta <- meta.process(dat.exp)
tbl <- meta.numEvents(meta)

immunoClust documentation built on Nov. 8, 2020, 5:19 p.m.