FCS-class: FCS class definition
In tchitchek-lab/CytoBackBone: Merging of phenotype information from different cytometric profiles
Description
FCS are S4 objects containing marker cell expressions obtained from cytometry profiles.
Details
This object mainly stores for each cell the intensities of all cell markers.
The slot 'trans.para' is a named list contains different parameters depending of the transformation applied on the marker expression intensities. The scale (cofactor) of the arcsinh transformation function is parametrized using the 'arcsinh.scale' value. The shift of the log transformation function is parametrized using the 'log.shift' value and the base of the log transformation function is parametrized using the 'log.base' value. If no transformation function have been applied, the 'trans.para' slot is set to NULL.
Slots
namea character indicating the internal name of the FCS object
profilesa character vector containing the names of the FCS profiles
cell.nban integer value indicating the number of FCS profiles
markersa character vector containing the marker names
markers.nban integer value indicating the number of markers
intensitiesa numeric matrix containing the intensities of each marker for each FCS profile
transa character specifying the name of a transformation function applied on the marker expression intensities. Possible values are "arcsinh" for arc sin hyperbolic transformation, "log" for logarithmic transformation, or "none" for no transformation
trans.paraa named list containing parameters of the transformation. Please refer to the details section for more details
trans.excludea character vector containing the marker names for which no transformation has been applied on
tchitchek-lab/CytoBackBone documentation built on May 28, 2019, 7:52 a.m.
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Description
FCS are S4 objects containing marker cell expressions obtained from cytometry profiles.
Details
This object mainly stores for each cell the intensities of all cell markers.
The slot 'trans.para' is a named list contains different parameters depending of the transformation applied on the marker expression intensities. The scale (cofactor) of the arcsinh transformation function is parametrized using the 'arcsinh.scale' value. The shift of the log transformation function is parametrized using the 'log.shift' value and the base of the log transformation function is parametrized using the 'log.base' value. If no transformation function have been applied, the 'trans.para' slot is set to NULL.
Slots
namea character indicating the internal name of the FCS object
profilesa character vector containing the names of the FCS profiles
cell.nban integer value indicating the number of FCS profiles
markersa character vector containing the marker names
markers.nban integer value indicating the number of markers
intensitiesa numeric matrix containing the intensities of each marker for each FCS profile
transa character specifying the name of a transformation function applied on the marker expression intensities. Possible values are "arcsinh" for arc sin hyperbolic transformation, "log" for logarithmic transformation, or "none" for no transformation
trans.paraa named list containing parameters of the transformation. Please refer to the details section for more details
trans.excludea character vector containing the marker names for which no transformation has been applied on
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