PISCESActivity: Generates protein activity readout using the NaRnEA...
In califano-lab/PISCES: Protein Activity Inferecne in Single Cells
PISCESActivity R Documentation
Generates protein activity readout using the NaRnEA algorithm.
Uses either the GES object found in the 'misc' field of the 'PISCESpact' assay or
the 'scale.data' field of the 'PISCESgexp' assay.
Description
Generates protein activity readout using the NaRnEA algorithm.
Uses either the GES object found in the 'misc' field of the 'PISCESpact' assay or
the 'scale.data' field of the 'PISCESgexp' assay.
Usage
PISCESActivity(pisces.obj, net.list, sample.weights = TRUE, use.sct = FALSE)
Arguments
pisces.obj
Seurat object w/ the 'PISCESpact' assay.
net.list
List of networks. If not specified, networks in the 'misc' field of the 'PISCESpact' assay will be used.
sample.weights
Flag to compute sample-specific weights. Default of TRUE.
use.sct
Flag to use the SCT matrix as a GES. Default of FALSE.
Value
Seurat object with 'PES' matrix in 'scale.data' of 'PISCESpact' assay.
'NES' results will be stored in the 'misc' field of the 'PISCESpact' assay.
califano-lab/PISCES documentation built on Jan. 11, 2023, 5:34 a.m.
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| PISCESActivity | R Documentation |
Generates protein activity readout using the NaRnEA algorithm. Uses either the GES object found in the 'misc' field of the 'PISCESpact' assay or the 'scale.data' field of the 'PISCESgexp' assay.
Description
Generates protein activity readout using the NaRnEA algorithm. Uses either the GES object found in the 'misc' field of the 'PISCESpact' assay or the 'scale.data' field of the 'PISCESgexp' assay.
Usage
PISCESActivity(pisces.obj, net.list, sample.weights = TRUE, use.sct = FALSE)
Arguments
pisces.obj |
Seurat object w/ the 'PISCESpact' assay. |
net.list |
List of networks. If not specified, networks in the 'misc' field of the 'PISCESpact' assay will be used. |
sample.weights |
Flag to compute sample-specific weights. Default of TRUE. |
use.sct |
Flag to use the SCT matrix as a GES. Default of FALSE. |
Value
Seurat object with 'PES' matrix in 'scale.data' of 'PISCESpact' assay. 'NES' results will be stored in the 'misc' field of the 'PISCESpact' assay.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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