run.RCTD: Runs the RCTD pipeline on a 'RCTD' object
In dmcable/RCTD: SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics
run.RCTD R Documentation
Runs the RCTD pipeline on a RCTD object
Description
Equivalent to sequentially running the functions fitBulk, choose_sigma_c, and fitPixels
Usage
run.RCTD(RCTD, doublet_mode = "doublet")
Arguments
RCTD
an RCTD object created using the create.RCTD function.
Details
If in doublet mode, fits at most two cell types per pixel. It classifies each pixel as 'singlet' or 'doublet' and searches for the cell types
on the pixel. If in full mode, can fit any number of cell types on each pixel. In multi mode, cell types are added using a greedy algorithm,
up to a fixed number.
Value
an RCTD object containing the results of the RCTD algorithm. Please see RCTD
documentation for more information on interpreting the content of the RCTD object.
dmcable/RCTD documentation built on Feb. 24, 2024, 11:03 p.m.
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| run.RCTD | R Documentation |
Runs the RCTD pipeline on a RCTD object
Description
Equivalent to sequentially running the functions fitBulk, choose_sigma_c, and fitPixels
Usage
run.RCTD(RCTD, doublet_mode = "doublet")
Arguments
RCTD |
an |
Details
If in doublet mode, fits at most two cell types per pixel. It classifies each pixel as 'singlet' or 'doublet' and searches for the cell types on the pixel. If in full mode, can fit any number of cell types on each pixel. In multi mode, cell types are added using a greedy algorithm, up to a fixed number.
Value
an RCTD object containing the results of the RCTD algorithm. Please see RCTD
documentation for more information on interpreting the content of the RCTD object.
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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