R/example_transcriptome_results.R
example_transcriptome_results.Rd
Example celltype enrichment results produced by ewce_expression_data.
example_transcriptome_results(verbose = TRUE, localHub = FALSE)
## Load the single cell data
ctd <- ewceData::ctd()
## Set the parameters for the analysis
## Use 3 bootstrap lists for speed, for publishable analysis use >10,000
reps <- 3
annotLevel <- 1 # <- Use cell level annotations (i.e. Interneurons)
## Use 5 up/down regulated genes (thresh) for speed, default is 250
thresh <- 5
## Load the top table
tt_alzh <- ewceData::tt_alzh()
tt_results <- EWCE::ewce_expression_data( sct_data = ctd, tt = tt_alzh, annotLevel = 1, thresh = thresh, reps = reps, ttSpecies = "human", sctSpecies = "mouse" )
save(tt_results, file = "inst/extdata/tt_results.rda")
List with 5 items.
tt_results <- EWCE::example_transcriptome_results()
#> Loading precomputed example transcriptome results.