RCTD.replicates-class: An S4 class used to store multiple replicates as 'SpatialRNA'...

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

An S4 class used to store multiple replicates as SpatialRNA objects.

Description

By storing multiple SpatialRNA replicates in this one object, it is convenient to run RCTD and CSIDE across all replicates. Finally, multiple replicates can be combined with population-level differential expression inference using the CSIDE.population.inference function

Details

Created using the create.RCTD.replicates or merge_RCTD_objects functions. One can run RCTD using the run.RCTD.replicates function, and one can run CSIDE using the run.CSIDE.replicates function.

Slots

RCTD.reps

a list of RCTD objects, one for each replicate

population_de_results

A list, indexed by cell type, of dataframes summarizing population-level differential expression for each genes. Relevant columns include: tau, variance across replicates; log_fc_est, the estimated differential expresison; sd_est, the standard error of estimated DE

population_sig_gene_list

A list, indexed by cell type, of vectors of significant genes

population_sig_gene_df

A list, indexed by cell type, of dataframe summarizing population-level differential expression for each signifcant gene, similar to population_de_results. Additionally, contains p (representing p-values) and q_val (representing q-values).

groups_ids

a named integer vector (length number of replicates) containing the group id for each replicate. Names represent the replicate names, and replicates of the same group will be expected to be more similar than replicates across groups

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