run.RCTD.replicates: Runs the RCTD pipeline on a 'RCTD.replicates' object

In dmcable/RCTD: SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics

Runs the RCTD pipeline on a RCTD.replicates object

Description

For each SpatialRNA replicate in the RCTD.replicates object, runs the run.RCTD function to assign cell types.

Usage

run.RCTD.replicates(RCTD.replicates, doublet_mode = "doublet")

Arguments

RCTD.replicates	an RCTD.replicates object created using the create.RCTD.replicates function.
doublet_mode	character string, either "doublet", "multi", or "full" on which mode to run RCTD. Please see above description.

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.replicates object containing the results of the RCTD algorithm. Please see RCTD.replicates and RCTD documentation for more information on interpreting the content of this object.

dmcable/RCTD documentation built on Feb. 24, 2024, 11:03 p.m.